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Yang J, Liu Y, Shang J, Chen Q, Chen Q, Ren L, Zhang N, Yu Y, Li Z, Song Y, Yang S, Scherer A, Tong W, Hong H, Xiao W, Shi L, Zheng Y. The Quartet Data Portal: integration of community-wide resources for multiomics quality control. Genome Biol 2023; 24:245. [PMID: 37884999 PMCID: PMC10601216 DOI: 10.1186/s13059-023-03091-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
The Quartet Data Portal facilitates community access to well-characterized reference materials, reference datasets, and related resources established based on a family of four individuals with identical twins from the Quartet Project. Users can request DNA, RNA, protein, and metabolite reference materials, as well as datasets generated across omics, platforms, labs, protocols, and batches. Reproducible analysis tools allow for objective performance assessment of user-submitted data, while interactive visualization tools support rapid exploration of reference datasets. A closed-loop "distribution-collection-evaluation-integration" workflow enables updates and integration of community-contributed multiomics data. Ultimately, this portal helps promote the advancement of reference datasets and multiomics quality control.
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Affiliation(s)
- Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, Guangdong, China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qiaochu Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zhihui Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yueqiang Song
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Shengpeng Yang
- Intelligent Storage, Alibaba Cloud, Alibaba Group, Hangzhou, Zhejiang, China
| | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Wenming Xiao
- Office of Oncological Diseases, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
- International Human Phenome Institutes (Shanghai), Shanghai, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
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