The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Binsheng Road 3333#, Hangzhou, Zhejiang, 310052, China.
The College of Biomedical Engineering and Instrument Science, Zhejiang University, Zhejiang, China.
Orphanet J Rare Dis. 2021 Feb 25;16(1):101. doi: 10.1186/s13023-021-01741-4.
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. A map for visualizing, locating and navigating rare diseases based on similarity will help clinicians and researchers understand and easily explore these diseases.
A 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.
A 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.
RDmap 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.
许多罕见人类遗传疾病的表型特征和分子基础十分复杂，这使得临床医生的诊断颇具挑战。基于相似性可视化、定位和导航罕见疾病的图谱，将有助于临床医生和研究人员理解并轻松探索这些疾病。
通过基于人类表型本体（HPO）和基因本体（GO）计算表型和致病基因之间的定量距离，对孤儿网上包含的罕见疾病的距离矩阵进行了测量，并将每种疾病映射到欧几里得空间。基于 ECharts 开发了一个增强了聚类类别和疾病信息的罕见疾病图谱。
我们发布了一个名为 RDmap 的罕见疾病图谱，网址为 http://rdmap.nbscn.org。基于表型的图谱共纳入 3287 种罕见疾病，基于基因的图谱共纳入 3789 种罕见遗传疾病；两个图谱之间连接了 1718 种重叠疾病。RDmap 的工作方式类似于广泛使用的 Google Map 服务，支持缩放和平移。在计算机评估中，表型相似性基础疾病定位功能优于传统的关键字搜索，20 个罕见疾病的案例也表明 RDmap 可以帮助临床医生寻找罕见疾病的诊断。
RDmap 是第一个用户交互的图谱式罕见疾病知识库。它将帮助临床医生和研究人员探索日益复杂的罕见遗传疾病领域。
