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Video Tip of the Week: PhenomeCentral

Silos. This is a big problem for us with human genome data from individuals. We’re getting sequences, but they are locked up in various ways. David Haussler’s talk at the recent Global Alliance for Genomics and Health meeting (GA4GH) emphasized this barrier, and also talked about ways they are looking to work around the legal, social, and institutional barriers that we’ve created. He talked about Beacon, which I highlighted recently as a Tip of the Week. But there are other strategies needed to connect physicians and patients with other folks who might help them get to answers. Heidi Rehm’s talk provided information about a possible tool for this: PhenomeCentral.

Unfortunately, the videos aren’t uploaded to YouTube, you have to go to the June 10 Meeting page and obtain them from there. The one that contained the information on PhenomeCentral is the one called “Matchmaker Exchange”.

PhenomeCentralLogoThe mission of PhenomeCentral, according to their site, is:

PhenomeCentral is a repository for secure data sharing targeted to clinicians and scientists working in the rare disorder community. PhenomeCentral encourages global scientific collaboration while respecting the privacy of patients profiled in this centralized database.

Certainly people in bioinformatics are familiar with the really crucial information from OMIM and Orphanet. But these are aggregators of information, not patient-specific. There may be lists of features of a condition, but how they appear in a given patient’s situation might vary.

What this new strategy will do is let doctors and researchers take the phenotype and genotype data (you can upload VCF files), and make predictions about the genes involved. They also have ways to “matchmake” possibly similar disease manifestations. This project is part of the larger “MatchMaker Exchange” collection (Note: MME is not a dating site…it’s also still under development). But the idea is that with patient details one could search for matches with other similar patients (depending on the privacy level of the records, of course). It sounded to me like a kind of BLAST for medical conditions (they didn’t call it that). But it also has ways to semantically link phenotype concepts, because they might be entered differently by different evaluating physicians, yet be the same type of issue underneath. That Human Phenotype Ontology (HPO) that I’ve covered a couple of times lately enables this.

They have 3 levels of privacy settings included: private, matchable (where you can find it in a search, but it’s not wide open to everyone), and public.

So although I used the GA4GH talk as a launching point to learn more about the features and conceptual parts of the PhenomeCentral software, I also came across this other webinar that was more specific about the software features (which is what I typically prefer for our tips, the specific software tools). The Genetic Alliance is a patient-centric group interested in answers for genetic and genome-variant medical situations, actively working with advocacy groups and researchers to bridge the needs of both. In their webinar series last year they included PhenomeCentral.

What I didn’t realize from the GA4GH overview was that there are additional tools, including a pedigree tool in the PhenoTips part. We find a lot of people find our blog searching for pedigree tools, so I wanted to be sure to mention that specifically. You can try it out by entering fake data in the playground over there, and accessing the Pedigree Tool from that record. This was also handy for me because I didn’t create a login for the main PhenomeCentral site due to the privacy issues.

So have a look at PhenomeCentral. And from the GA4GH video I learned that there is a special journal issue coming up in the fall that will have papers related to these projects. So I’ll link to the PhenoTips publication below now, but when more references become available for this tool or project I’ll add them in. I expect there will be metrics about algorithms in use and other technical details that are important for fully evaluating the tool.

Quick links:

PhenomeCentral: https://phenomecentral.org/

PhenoTips: https://phenotips.org/ (has the playground + pedigree tool)

GA4GH videos: http://genomicsandhealth.org/news-events/events/june-10th-meeting-presentations

References:
Girdea, M., Dumitriu, S., Fiume, M., Bowdin, S., Boycott, K., Chénier, S., Chitayat, D., Faghfoury, H., Meyn, M., Ray, P., So, J., Stavropoulos, D., & Brudno, M. (2013). PhenoTips: Patient Phenotyping Software for Clinical and Research Use Human Mutation, 34 (8), 1057-1065 DOI: 10.1002/humu.22347