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Showing posts from 2016

Why cross-species phenomics informatics is critical to the PMI

Genomics, electronic health records, participant-provided data, sensors, and mobile health technologies can all contribute to personalized medicine. However, we currently cannot achieve statistical correlations amongst these almost unlimited number of parameters that will be collected by the PMI and the depth of mechanistic understanding that will be required for treatment stratification and the development of novel, targeted therapies. The promise of personalized medicine requires deep knowledge of the relationships between genotype, phenotype, and environmental variables - but we simply don’t have enough data. For example, in the ExAC database there are 3,230 genes with near-complete depletion of predicted protein-truncating variants, where 72% of these genes having no currently established human disease phenotype. If we look across organisms, we see that of these 2311 genes with unknown causal phenotypes/diseases, 88% have an associated phenotype in an ortholog, with 56% having or…

Monarch's Phenogrid widget provides similarity visualizations for the International Mouse Phenotyping Consortium.

Monarch's Phenogrid phenotype comparison tool is now available for phenotype profile comparisons on the International Mouse Phenotype Consortium ( site.

Visitors to the IMPC site can find Phenogrid comparisons on disease pages such as the entry for Pfeiffer Syndrome.  Under the mouse models, you will see a plus ("+") symbol at the end of each row:

Clicking on that plus sign will reveal the Phenogrid widget showing mouse strains  with phenotype profiles similar to those of the gene in question. For Pfeiffer, the grid will reveal multiple variants of Fgfr1, illustrating differences in phenotypes seen across these strains.  Mousing over the cells will show the details of the match between the given phenotype and the model:

Mousing over the model label will lead to the display of a dialog box with listings of the specific genotype of the model and relevant phenotypes, all of which can be clicked to access  pages with additional detail.

As with other pheno…

Finally, a medical terminology that patients, doctors, and machines can all understand.

By Nicole Vasilevsky, Mark Engelstad, Erin Foster, Julie McMurry, Chris Mungall, Peter Robinson, Sebastian Köhler, Melissa Haendel
For many patients with rare and undiagnosed diseases, getting an accurate diagnosis, or even finding the appropriate experts is a long and winding road. To accelerate and facilitate this process, we developed a medical vocabulary (“HPO”) which is comprised of 12,000 terms that doctors can use to codify the precise and distinct observations about patients and their conditions. The HPO is structured in a way that enables machines to intelligently compare a patient’s profile with what scientists worldwide have already uncovered about diseases and their genetic causes.
Until now, most of the HPO labels and synonyms were composed of clinical terms unfamiliar to patients. For example, a patient may know they are ‘color-blind’, but may not be familiar with the clinical term ‘Dyschromatopsia’. This is why we developed a layer of 5,000 corresponding terms that can b…

European Rare Disease Organization recognizes Dr. Peter Robinson for scientific excellence

Peter Robinson from Charite - Universit√§tsmedizin Berlin, received the prestigious European Rare Disease Organization (EURODIS) Scientific Award on “Rare Disease Day”, February 23, 2016. EURODIS is a non-governmental organization that provides an alliance for patients with rare diseases in Europe and beyond. This Scientific Award recognizes his scientific excellence and his support of the patient community through the work he does with the Human Phenotype Ontology and the Monarch Initiative, the world’s largest gene-phenotype knowledgebase. Dr. Robinson attended the award ceremony in Brussels, Belgium, where he received the award from the distinguished guest, HRH Princess Astrid of Belgium. Only 8 awards are given, and there were 350 nominations this year. We at Monarch could not be more proud!