diseaseGPS: auxiliary diagnostic system for genetic disorders based on genotype and phenotype
Daoyi Huang, Jianping Jiang, Tingting Zhao, Shengnan Wu, Pin Li, Yongfen Lyu, Jincai Feng, Mingyue Wei, Zhixing Zhu, Jianlei Gu, Yongyong Ren, Guangjun Yu, Hui Lu- Computational Mathematics
- Computational Theory and Mathematics
- Computer Science Applications
- Molecular Biology
- Biochemistry
- Statistics and Probability
Abstract
Summary
The next-generation sequencing brought opportunities for the diagnosis of genetic disorders due to its high throughput capabilities. However, the majority of existing methods were limited to only sequencing candidate variants, and the process of linking these variants to a diagnosis of genetic disorders still required medical professionals to consult databases. Therefore, we introduce diseaseGPS, an integrated platform for the diagnosis of genetic disorders that combines both phenotype and genotype data for analysis. It offers not only a user-friendly GUI web application for those without a programming background, but also scripts that can be executed in batch mode for bioinformatics professionals. The genetic and phenotypic data are integrated using the ACMG-Bayes method and a novel phenotypic similarity method, to prioritize the results of genetic disorders. diseaseGPS was evaluated on 6085 cases from Deciphering Developmental Disorders project and 187 cases from Shanghai Children’s hospital. The results demonstrated that diseaseGPS performed better than other commonly used methods.
Availability
diseaseGPS is available to freely accessed at https://diseasegps.sjtu.edu.cn with source code at https://github.com/BioHuangDY/diseaseGPS.
Supplementary information
Supplementary data are available at Bioinformatics online.