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How does PhenIX work?

PhenIX, Phenotypic Interpretation of eXomes, is a pipeline for ranking (prioritizing) candidate genes in exomes or NGS panels with comprehensive coverage of human Mendelian disease genes. It ranks genes based on predicted variant pathogenicity as well as phenotypic similarity of diseases associated with the genes harboring these variants to the phenotypic profile of the individual being investigated, based on analysis powered by the Human Phenotype Ontology (HPO).

What input does PhenIX require?

PhenIX requires a VCF file mapped to hg19/Gchr37, as well as a list of HPO terms representing the phenotype observed in the patient. The PhenIX server is designed to work with single sample VCF files, but locally installable versions are available on a collaborative basis that offer additional functionality for pedigree filtering and prioritization based on other data sources.

Run PhenIX online:

After you submit your data, the VCF file, the HPO terms, and the other parameters will be uploaded to our server. Do not hit the refresh or back button during this time.

Human Phenotype Ontology (HPO) terms are autocompleted (e.g. typing 'polyd' will autocomplete to 'polydactyly'). Users can enter the term name (e.g., "Dry skin") or a synonym (e.g., "Xerosis"). In the case of problems in trying to find the correct HPO term, we recommend using the PhenExplorer tool. HPO IDs from PhenExplorer can directly serve as inputs to PhenIX.
The input VCF file is stored with memory and not written to a hard disk. Neither the sequence data nor the phenotype data is stored for longer than the HTTP session. PhenIX is freely available for academic users or for private use. Other users are requested to contact us to obtain a license.