PICOTEES: a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants from Chinese children cohorts.

Autor: Dong X; Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China., Lu Y; Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China., Guo L; Department of Bioinformatics, Hangzhou Nuowei Information Technology Co., Ltd, Hangzhou, Zhejiang 310000, China., Li C; Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China., Ni Q; Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China., Wu B; Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China., Wang H; Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China., Yang L; Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China., Wu S; The Third Research Institute of the Ministry of Public Security, Shanghai 200031, China., Sun Q; Department of Bioinformatics, Hangzhou Nuowei Information Technology Co., Ltd, Hangzhou, Zhejiang 310000, China., Zheng H; Department of Bioinformatics, Hangzhou Nuowei Information Technology Co., Ltd, Hangzhou, Zhejiang 310000, China., Zhou W; Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Xiamen Campus of Children's Hospital of Fudan University, Xiamen, Fujian 361006, China. Electronic address: zhouwenhao@fudan.edu.cn., Wang S; Department of Bioinformatics, Hangzhou Nuowei Information Technology Co., Ltd, Hangzhou, Zhejiang 310000, China; Institutes for Systems Genetics, West China Hospital, Chengdu, Sichuan 610041, China; Shanghai Putuo People's Hospital, Tongji University, Shanghai 200060, China. Electronic address: shuang.wang@nvxclouds.com.
Jazyk: angličtina
Zdroj: Journal of genetics and genomics = Yi chuan xue bao [J Genet Genomics] 2024 Feb; Vol. 51 (2), pp. 243-251. Date of Electronic Publication: 2023 Sep 13.
DOI: 10.1016/j.jgg.2023.09.003
Abstrakt: The growth in biomedical data resources has raised potential privacy concerns and risks of genetic information leakage. For instance, exome sequencing aids clinical decisions by comparing data through web services, but it requires significant trust between users and providers. To alleviate privacy concerns, the most commonly used strategy is to anonymize sensitive data. Unfortunately, studies have shown that anonymization is insufficient to protect against reidentification attacks. Recently, privacy-preserving technologies have been applied to preserve application utility while protecting the privacy of biomedical data. We present the PICOTEES framework, a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants (https://birthdefectlab.cn:3000/). PICOTEES enables privacy-preserving queries of the phenotype spectrum for a single variant by utilizing trusted execution environment technology, which can protect the privacy of the user's query information, backend models, and data, as well as the final results. We demonstrate the utility and performance of PICOTEES by exploring a bioinformatics dataset. The dataset is from a cohort containing 20,909 genetic testing patients with 3,152,508 variants from the Children's Hospital of Fudan University in China, dominated by the Chinese Han population (>99.9%). Our query results yield a large number of unreported diagnostic variants and previously reported pathogenicity.
Competing Interests: Conflict of interest We declare that the authors have no conflict of interest that might be perceived to influence the results and/or discussion reported in this paper.
(Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)
Databáze: MEDLINE
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