myPhenoDB is a freely-accessible website that allow clinical researchers to store standardized phenotypic information, diagnosis, and pedigree data and then run analyses on VCF files from individuals, families or cohorts with suspected Mendelian disease. This web site is intended for interested researchers to test it on their samples before downloading the software for their own institutional use or for those researchers who do not have access to robust IT support.
This website is hosted at Johns Hopkins University (JHU) and is HIPAA compliant and secure, but only de-identifed data should be loaded onto this website. In order to use myPhenoDB, you must create an account, and only your data will be accessible to you. Only the site administrator has access to all the data. If you wish to load a VCF file for analysis, it will be immediately converted to an ANNOVAR file. The ANNOVAR file will be available to you for 24 hours to run any analysis that you wish. After the 24 hours, the ANNOVAR file will be deleted, but your final result table (of the analyses that you ran) will remain on the site. You may redo an analysis at any time by re-uploading a VCF file. The ANNOVAR conversion software comes from OpenBioinformatics and may only be used by academic users. No commercial use is permitted by their license.
If your analysis does not result in a conclusive answer, you may push your final result gene list to GeneMatcher to see if anyone else has an individual or family with the same gene on their candidate list. Please see GeneMatcher for details of how that site functions.
Those who wish to download PhenoDB to their institutions may do so from the 'Downloads' tab at the top of the page. You must register to download as we wish to inform you of upgrades to the software. Also, PhenoDB may be used as the de-identified site that is here, with no ability to upload images, or may be toggled to a version with the ability to have identifiers, upload any type of image, and share data freely or with restrictions. The phenotype and analysis modules are included. This version of PhenoDB is a good choice for clinics or labs wishing to collect standardized phenotypic and genomic data. Those who wish to use PhenoDB as a research tool may prefer to download researchPhenoDB. This software also includes sample tracking and consent storage (ELSI) modules that may be useful to a project.
myPhenoDB was developed by the Baylor-Hopkins Center for Mendelian Genomics at the McKusick-Nathans Institute of Genetic Medicine at JHU funded by the NHGRI. The website is supported by the Sutland-Pakula family.
If you are publishing a paper that uses myPhenoDB, please state this in the paper and cite myPhenoDB:
Sobreira N, Schiettecatte F, Boehm C, Valle D, Hamosh A. New tools for Mendelian disease gene identification: PhenoDB variant analysis module; and GeneMatcher, a web-based tool for linking investigators with an interest in the same gene. Hum Mutat. 2015 Apr;36(4):425-31. doi: 10.1002/humu.22769. PubMed: 25684268.
Another paper that discusses myPhenoDB is:
Sobreira N, Schiettecatte F, Boehm C, Valle D, Hamosh A. PhenoDB: a new web-based tool for the collection, storage, and analysis of phenotypic features. Hum Mutat. 2013 Apr;34(4):566-71. doi: 10.1002/humu.22283. Epub 2013 Mar 4. PubMed: 23378291.
Additional information is available in the Frequently Asked Questions (FAQs).