DiseaseGPS: Auxiliary Diagnostic System for Genetic Disorders Based on Genotype and Phenotype

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2023 Aug 30

PMID 37647638

Authors

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

Affiliations

Soon will be listed here.

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 And Implementation: diseaseGPS is available to freely accessed at https://diseasegps.sjtu.edu.cn with source code at https://github.com/BioHuangDY/diseaseGPS.

Citing Articles

Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond.

Leist I, Rivas-Torrubia M, Alarcon-Riquelme M, Barturen G, Consortium P, Gut I BMC Bioinformatics. 2024; 25(1):373.

PMID: 39633268 PMC: 11616229. DOI: 10.1186/s12859-024-05993-2.

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