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RDmap: a map for exploring rare diseases.

Jian Yang1,2, Cong Dong1,2, Huilong Duan2

  • 1The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Binsheng Road 3333#, Hangzhou, Zhejiang, 310052, China.

Orphanet Journal of Rare Diseases
|February 26, 2021
PubMed
Summary
This summary is machine-generated.

RDmap is a novel interactive map for rare diseases, aiding diagnosis by visualizing similarities between phenotypes and genes. This tool helps clinicians and researchers navigate complex genetic conditions more effectively.

Keywords:
Clinical decision supportDisease mapPathogenetic genePhenotypeRare disease

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Area of Science:

  • Genetics
  • Medical Informatics
  • Bioinformatics

Background:

  • Rare human genetic diseases present diagnostic challenges due to complex phenotypes and molecular bases.
  • Effective visualization and navigation tools are needed for clinicians and researchers to explore rare diseases.

Purpose of the Study:

  • To develop an interactive, map-style knowledgebase for rare diseases to aid in diagnosis and exploration.
  • To create a user-friendly platform for navigating complex genetic conditions.

Main Methods:

  • Calculated quantitative distances between phenotypes and pathogenic genes using Human Phenotype Ontology (HPO) and Gene Ontology (GO).
  • Mapped rare diseases into Euclidean space to create a distance matrix.
  • Developed an interactive rare disease map (RDmap) using ECharts, incorporating clustering and disease information.

Main Results:

  • Launched RDmap (http://rdmap.nbscn.org) with phenotype-based (3287 diseases) and gene-based (3789 diseases) maps.
  • RDmap supports interactive features like zooming and panning, similar to Google Maps.
  • In silico evaluation showed phenotype similarity outperformed keyword searches; case studies confirmed RDmap's utility in rare disease diagnosis.

Conclusions:

  • RDmap is the first user-interactive, map-style knowledgebase for rare diseases.
  • This tool facilitates exploration of rare genetic diseases for clinicians and researchers.
  • RDmap enhances understanding and diagnosis of rare genetic conditions.