Monarch Initiative’s Efforts Help Rare Disease Researchers and Patients

3 min readFeb 28, 2023

Image credit: CU Anschutz Medical Campus

With the aim of improving diagnosis and, ultimately, treatment, the Monarch Initiative and the Phenomics First Center of Excellence in Genomic Science (CEGS) bring together basic science knowledge, clinical research and rare disease patients to help untangle the causes and characteristics of rare diseases.

There are more than 10,000 different rare diseases (see our commentary in Nature Reviews Drug Discovery). Each rare disease may affect a relatively small number of people, but if you add up all the rare diseases, they affect about 10% of the population, which is a lot of people! Though they may be undiagnosed, all of us almost certainly know someone who has a rare disease.

In order to properly recognize and classify rare diseases, it is important to have precise definitions for each. This is the focus of our unified Mondo Disease Ontology. The Mondo developers continually collaborate with the rare disease community, including patients, clinicians, and researchers, to help improve Mondo’s depth and coverage of rare diseases.

Tools and standards developed by the Monarch Initiative played key roles in the recent 100,000 Genomes Project, which studied the genomes of patients affected by rare disease or cancer. The Human Phenotype Ontology (HPO) was used to encode the clinical data and the diagnostic pipeline used in the study made use of our Exomiser variant prioritization tool, which helps diagnose rare diseases. Exomiser’s ontology-driven phenotype matching algorithm can identify patients who have an atypical profile for a disease, helping to solve some of the toughest cases. In this study, Exomiser found 88% of the rare disease diagnoses in its top five ranked disease candidates. The American Journal of Human Genetics selected this study as one of the top 10 advances in genomic medicine for 2022.

The Phenopacket standard, which recently attained ISO approval, is a much-needed approach to storing and sharing phenotypic data in standardized formats that can be parsed by humans and machines. Phenopackets are quickly becoming the preferred way to capture clinical data and integrate it with genomic data to help enable precision medicine and rare disease diagnosis.

Monarch’s efforts in the rare disease arena are being recognized. The National Organization for Rare Disorders (NORD) recently named the University of Colorado Anschutz Medical Campus (headquarters for Monarch) a Rare Disease Center of Excellence. We received a “Distinguished Achievement Award for Data Reuse” in the first NIH DataWorks! Challenge.

Monarch Initiative’s Efforts Help Rare Disease Researchers and Patients

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Written by Monarch Initiative