RDmap: a map for exploring rare diseases

Jian Yang,Cong Dong,Haomin Li,Huilong Duan,Qiang Shu

doi:10.1186/s13023-021-01741-4

Jian Yang, Cong Dong + Show 3 more

Open Access

https://doi.org/10.1186/s13023-021-01741-4

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Abstract

BackgroundThe complexity of the phenotypic characteristics and molecular bases of many rare human genetic diseases makes the diagnosis of such diseases a challenge for clinicians. A map for visualizing, locating and navigating rare diseases based on similarity will help clinicians and researchers understand and easily explore these diseases.MethodsA distance matrix of rare diseases included in Orphanet was measured by calculating the quantitative distance among phenotypes and pathogenic genes based on Human Phenotype Ontology (HPO) and Gene Ontology (GO), and each disease was mapped into Euclidean space. A rare disease map, enhanced by clustering classes and disease information, was developed based on ECharts.ResultsA rare disease map called RDmap was published at http://rdmap.nbscn.org. Total 3287 rare diseases are included in the phenotype-based map, and 3789 rare genetic diseases are included in the gene-based map; 1718 overlapping diseases are connected between two maps. RDmap works similarly to the widely used Google Map service and supports zooming and panning. The phenotype similarity base disease location function performed better than traditional keyword searches in an in silico evaluation, and 20 published cases of rare diseases also demonstrated that RDmap can assist clinicians in seeking the rare disease diagnosis.ConclusionRDmap is the first user-interactive map-style rare disease knowledgebase. It will help clinicians and researchers explore the increasingly complicated realm of rare genetic diseases.

Highlights

The complexity of the phenotypic characteristics and molecular bases of many rare human genetic diseases makes the diagnosis of such diseases a challenge for clinicians
The locations reflect the distance among diseases, and the size of the points reflect the prevalence of rare diseases. a Rare disease map and clusters based on phenotype
We aimed to propose a method to construct two rare human disease maps based on the semantic similarities of both phenotypic characteristics and pathogenetic genes of rare diseases

Summary

Introduction

The complexity of the phenotypic characteristics and molecular bases of many rare human genetic diseases makes the diagnosis of such diseases a challenge for clinicians. Rare diseases commonly with a prevalence of less than 5 in 10,000 people [1], most of which are caused by underlying genetic factors, often manifest in infants or young children and affect the patients’ whole life. These conditions are rare, studies involving them have revealed important insights about normal physiology that, in turn, have provided a better understanding of common disorders, universal mechanisms, critical pathways, and therapies that are useful to treat more than one disease. More detail about the disease clusters and their relationships were available in the supplemental materials

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