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

Xinran Dong; Yulan Lu; Lanting Guo; Chuan Li; Qi Ni; Bingbing Wu; Huijun Wang; Lin Yang; Songyang Wu; Qi Sun; Hao Zheng; Wenhao Zhou; Shuang Wang

doi:10.1016/j.jgg.2023.09.003

Volume 51 Issue 2

Feb. 2024

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Article Navigation > Journal of Genetics and Genomics > 2024 > 51(2): 243-251

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

doi: 10.1016/j.jgg.2023.09.003

a. Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China;
b. Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China;
c. Department of Bioinformatics, Hangzhou Nuowei Information Technology Co., Ltd, Hangzhou, Zhejiang 310000, China;
d. The Third Research Institute of the Ministry of Public Security, Shanghai 200031, China;
e. Xiamen Campus of Children's Hospital of Fudan University, Xiamen, Fujian 361006, China;
f. Institutes for Systems Genetics, West China Hospital, Chengdu, Sichuan 610041, China;
g. Shanghai Putuo People's Hospital, Tongji University, Shanghai 200060, China

Funds:

D Program of Zhejiang (No. 2022C01126 to Q. Sun and S. Wang), and National Key R&

D Program of China (2022ZD0116003 to X. Dong), the Science and Technology Commission of Shanghai (22002400700 to S. Wu), Shanghai Municipal Science and Technology Major Project (20Z11900600 to W. Zhou), National Key Research and Development Program (2018YFC0116903 to W. Zhou), and Major Research Projects for Young and Middle-aged People of Fujian Province (2021ZQNZD017 to Y. Lu). This work is also supported by Key Lab Information Network Security, Ministry of Public Security (to H. Zheng and S. Wang), “Pioneer” and ”Leading Goose” R&

D Program of China (2021YFC2500802 and 2021YFC2500806 to H. Zheng and S. Wang). We thank all doctors and nurses in our hospital for their patient care and data collection. We are very grateful to the patient families for their trust in our lab.

This work was funded by the Shanghai Hospital Development Center (SHDC2020CR6028-002 to W. Zhou), National Key R&

D Program of China (2020YFC2006402 to Y. Lu), National Key R&

Received Date: 2023-04-06
Accepted Date: 2023-09-03
Rev Recd Date: 2023-08-31
Publish Date: 2023-09-13

Abstract

Abstract

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.
- Privacy protection,
- Rare diseases in children,
- Genetic testing,
- Web system,
- Trusted execution environment

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References(34)

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