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Huang J, Zhao Y, Meng B, Lu A, Wei Y, Dong L, Fang X, An D, Dai X. SEAOP: a statistical ensemble approach for outlier detection in quantitative proteomics data. Brief Bioinform 2024; 25:bbae129. [PMID: 38557674 PMCID: PMC10982946 DOI: 10.1093/bib/bbae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/01/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Quality control in quantitative proteomics is a persistent challenge, particularly in identifying and managing outliers. Unsupervised learning models, which rely on data structure rather than predefined labels, offer potential solutions. However, without clear labels, their effectiveness might be compromised. Single models are susceptible to the randomness of parameters and initialization, which can result in a high rate of false positives. Ensemble models, on the other hand, have shown capabilities in effectively mitigating the impacts of such randomness and assisting in accurately detecting true outliers. Therefore, we introduced SEAOP, a Python toolbox that utilizes an ensemble mechanism by integrating multi-round data management and a statistics-based decision pipeline with multiple models. Specifically, SEAOP uses multi-round resampling to create diverse sub-data spaces and employs outlier detection methods to identify candidate outliers in each space. Candidates are then aggregated as confirmed outliers via a chi-square test, adhering to a 95% confidence level, to ensure the precision of the unsupervised approaches. Additionally, SEAOP introduces a visualization strategy, specifically designed to intuitively and effectively display the distribution of both outlier and non-outlier samples. Optimal hyperparameter models of SEAOP for outlier detection were identified by using a gradient-simulated standard dataset and Mann-Kendall trend test. The performance of the SEAOP toolbox was evaluated using three experimental datasets, confirming its reliability and accuracy in handling quantitative proteomics.
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Affiliation(s)
- Jinze Huang
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China
| | - Yang Zhao
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Bo Meng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Ao Lu
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China
| | - Yaoguang Wei
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China
| | - Lianhua Dong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Dong An
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
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Dong L, Zhang Y, Fu B, Swart C, Jiang H, Liu Y, Huggett J, Wielgosz R, Niu C, Li Q, Zhang Y, Park SR, Sui Z, Yu L, Liu Y, Xie Q, Zhang H, Yang Y, Dai X, Shi L, Yin Y, Fang X. Reliable biological and multi-omics research through biometrology. Anal Bioanal Chem 2024:10.1007/s00216-024-05239-3. [PMID: 38507042 DOI: 10.1007/s00216-024-05239-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
Metrology is the science of measurement and its applications, whereas biometrology is the science of biological measurement and its applications. Biometrology aims to achieve accuracy and consistency of biological measurements by focusing on the development of metrological traceability, biological reference measurement procedures, and reference materials. Irreproducibility of biological and multi-omics research results from different laboratories, platforms, and analysis methods is hampering the translation of research into clinical uses and can often be attributed to the lack of biologists' attention to the general principles of metrology. In this paper, the progresses of biometrology including metrology on nucleic acid, protein, and cell measurements and its impacts on the improvement of reliability and comparability in biological research are reviewed. Challenges in obtaining more reliable biological and multi-omics measurements due to the lack of primary reference measurement procedures and new standards for biological reference materials faced by biometrology are discussed. In the future, in addition to establishing reliable reference measurement procedures, developing reference materials from single or multiple parameters to multi-omics scale should be emphasized. Thinking in way of biometrology is warranted for facilitating the translation of high-throughput omics research into clinical practices.
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Affiliation(s)
- Lianhua Dong
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
| | - Yu Zhang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Boqiang Fu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Claudia Swart
- Physikalisch-Technische Bundesanstalt, 38116, Braunschweig, Germany
| | | | - Yahui Liu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Jim Huggett
- National Measurement Laboratory at LGC (NML), Teddington, Middlesex, UK
| | - Robert Wielgosz
- Bureau International Des Poids Et Mesures (BIPM), Pavillon de Breteuil, 92312, Sèvres Cedex, France
| | - Chunyan Niu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Qianyi Li
- BGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yongzhuo Zhang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Sang-Ryoul Park
- Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Zhiwei Sui
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Lianchao Yu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | | | - Qing Xie
- BGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongfu Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xinhua Dai
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Ye Yin
- BGI, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xiang Fang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
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3
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Zhang N, Chen Q, Zhang P, Zhou K, Liu Y, Wang H, Duan S, Xie Y, Yu W, Kong Z, Ren L, Hou W, Yang J, Gong X, Dong L, Fang X, Shi L, Yu Y, Zheng Y. Quartet metabolite reference materials for inter-laboratory proficiency test and data integration of metabolomics profiling. Genome Biol 2024; 25:34. [PMID: 38268000 PMCID: PMC10809448 DOI: 10.1186/s13059-024-03168-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Various laboratory-developed metabolomic methods lead to big challenges in inter-laboratory comparability and effective integration of diverse datasets. RESULTS As part of the Quartet Project, we establish a publicly available suite of four metabolite reference materials derived from B lymphoblastoid cell lines from a family of parents and monozygotic twin daughters. We generate comprehensive LC-MS-based metabolomic data from the Quartet reference materials using targeted and untargeted strategies in different laboratories. The Quartet multi-sample-based signal-to-noise ratio enables objective assessment of the reliability of intra-batch and cross-batch metabolomics profiling in detecting intrinsic biological differences among the four groups of samples. Significant variations in the reliability of the metabolomics profiling are identified across laboratories. Importantly, ratio-based metabolomics profiling, by scaling the absolute values of a study sample relative to those of a common reference sample, enables cross-laboratory quantitative data integration. Thus, we construct the ratio-based high-confidence reference datasets between two reference samples, providing "ground truth" for inter-laboratory accuracy assessment, which enables objective evaluation of quantitative metabolomics profiling using various instruments and protocols. CONCLUSIONS Our study provides the community with rich resources and best practices for inter-laboratory proficiency tests and data integration, ensuring reliability of large-scale and longitudinal metabolomic studies.
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Affiliation(s)
- Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qiaochu Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Kejun Zhou
- Human Metabolomics Institute, Inc., Shenzhen, Guangdong, China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Shumeng Duan
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yongming Xie
- Shanghai Applied Protein Technology Co. Ltd, Shanghai, China
| | - Wenxiang Yu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ziqing Kong
- Calibra Diagnostics, Hangzhou, Zhejiang, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, Guangdong, China
| | | | | | - Xiang Fang
- National Institute of Metrology, Beijing, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
- International Human Phenome Institute, Shanghai, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
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Guo L, Wang L, Qin G, Zhang J, Peng J, Li L, Chen X, Wang D, Qiu J, Wang E. M-type pyruvate kinase 2 (PKM2) tetramerization alleviates the progression of right ventricle failure by regulating oxidative stress and mitochondrial dynamics. J Transl Med 2023; 21:888. [PMID: 38062516 PMCID: PMC10702013 DOI: 10.1186/s12967-023-04780-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Right ventricle failure (RVF) is a progressive heart disease that has yet to be fully understood at the molecular level. Elevated M-type pyruvate kinase 2 (PKM2) tetramerization alleviates heart failure, but detailed molecular mechanisms remain unclear. OBJECTIVE We observed changes in PKM2 tetramerization levels during the progression of right heart failure and in vitro cardiomyocyte hypertrophy and explored the causal relationship between altered PKM2 tetramerization and the imbalance of redox homeostasis in cardiomyocytes, as well as its underlying mechanisms. Ultimately, our goal was to propose rational intervention strategies for the treatment of RVF. METHOD We established RVF in Sprague Dawley (SD) rats by intraperitoneal injection of monocrotaline (MCT). The pulmonary artery pressure and right heart function of rats were assessed using transthoracic echocardiography combined with right heart catheterization. TEPP-46 was used both in vivo and in vitro to promote PKM2 tetramerization. RESULTS We observed that oxidative stress and mitochondrial disorganization were associated with increased apoptosis in the right ventricular tissue of RVF rats. Quantitative proteomics revealed that PKM2 was upregulated during RVF and negatively correlated with the cardiac function. Facilitating PKM2 tetramerization promoted mitochondrial network formation and alleviated oxidative stress and apoptosis during cardiomyocyte hypertrophy. Moreover, enhancing PKM2 tetramer formation improved cardiac mitochondrial morphology, mitigated oxidative stress and alleviated heart failure. CONCLUSION Disruption of PKM2 tetramerization contributed to RVF by inducing mitochondrial fragmentation, accumulating ROS, and finally promoted the progression of cardiomyocyte apoptosis. Facilitating PKM2 tetramerization holds potential as a promising therapeutic approach for RVF.
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Affiliation(s)
- Lizhe Guo
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Lu Wang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Gang Qin
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Junjie Zhang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Jin Peng
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Longyan Li
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiang Chen
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China
| | - Dandan Wang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders (Xiangya Hospital), Changsha, China
| | - Jian Qiu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders (Xiangya Hospital), Changsha, China.
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.
| | - E Wang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders (Xiangya Hospital), Changsha, China.
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Ren L, Duan X, Dong L, Zhang R, Yang J, Gao Y, Peng R, Hou W, Liu Y, Li J, Yu Y, Zhang N, Shang J, Liang F, Wang D, Chen H, Sun L, Hao L, Scherer A, Nordlund J, Xiao W, Xu J, Tong W, Hu X, Jia P, Ye K, Li J, Jin L, Hong H, Wang J, Fan S, Fang X, Zheng Y, Shi L. Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance. Genome Biol 2023; 24:270. [PMID: 38012772 PMCID: PMC10680274 DOI: 10.1186/s13059-023-03109-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome. RESULTS We established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data. CONCLUSIONS The Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.
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Affiliation(s)
- Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Xiaoke Duan
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | | | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, Guangdong, China
| | - Yuechen Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- Nextomics Biosciences Institute, Wuhan, Hubei, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Fan Liang
- Nextomics Biosciences Institute, Wuhan, Hubei, China
| | - Depeng Wang
- Nextomics Biosciences Institute, Wuhan, Hubei, China
| | - Hui Chen
- OrigiMed Co., Ltd, Shanghai, China
| | - Lele Sun
- Sequanta Technologies Co., Ltd, Shanghai, China
| | | | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
| | - Jessica Nordlund
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Wenming Xiao
- Office of Oncologic Diseases, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Xin Hu
- Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peng Jia
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Kai Ye
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Jing Wang
- National Institute of Metrology, Beijing, China.
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China.
| | - Xiang Fang
- National Institute of Metrology, Beijing, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- Shanghai Cancer Center, Fudan University, Shanghai, China
- International Human Phenome Institutes, Shanghai, China
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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] [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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7
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Yu Y, Hou W, Liu Y, Wang H, Dong L, Mai Y, Chen Q, Li Z, Sun S, Yang J, Cao Z, Zhang P, Zi Y, Liu R, Gao J, Zhang N, Li J, Ren L, Jiang H, Shang J, Zhu S, Wang X, Qing T, Bao D, Li B, Li B, Suo C, Pi Y, Wang X, Dai F, Scherer A, Mattila P, Han J, Zhang L, Jiang H, Thierry-Mieg D, Thierry-Mieg J, Xiao W, Hong H, Tong W, Wang J, Li J, Fang X, Jin L, Xu J, Qian F, Zhang R, Shi L, Zheng Y. Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling. Nat Biotechnol 2023:10.1038/s41587-023-01867-9. [PMID: 37679545 DOI: 10.1038/s41587-023-01867-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/15/2023] [Indexed: 09/09/2023]
Abstract
Certified RNA reference materials are indispensable for assessing the reliability of RNA sequencing to detect intrinsically small biological differences in clinical settings, such as molecular subtyping of diseases. As part of the Quartet Project for quality control and data integration of multi-omics profiling, we established four RNA reference materials derived from immortalized B-lymphoblastoid cell lines from four members of a monozygotic twin family. Additionally, we constructed ratio-based transcriptome-wide reference datasets between two samples, providing cross-platform and cross-laboratory 'ground truth'. Investigation of the intrinsically subtle biological differences among the Quartet samples enables sensitive assessment of cross-batch integration of transcriptomic measurements at the ratio level. The Quartet RNA reference materials, combined with the ratio-based reference datasets, can serve as unique resources for assessing and improving the quality of transcriptomic data in clinical and biological settings.
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Affiliation(s)
- Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | | | - Yuanbang Mai
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zhihui Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Shanyue Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, China
| | - Zehui Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yi Zi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ruimei Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jian Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
- Nextomics Biosciences Institute, Wuhan, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xiaolin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Tao Qing
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ding Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bingying Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bin Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Chen Suo
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yan Pi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xia Wang
- National Institute of Metrology, Beijing, China
| | | | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | - Pirkko Mattila
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | | | - Lijun Zhang
- Nanjing Vazyme Biotech Co. Ltd., Nanjing, China
| | | | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Wenming Xiao
- Office of Oncologic Diseases, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Jing Wang
- National Institute of Metrology, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China
- National Center of Gerontology, Beijing, China
| | - Xiang Fang
- National Institute of Metrology, Beijing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
| | - Feng Qian
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China.
- National Center of Gerontology, Beijing, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
- International Human Phenome Institutes, Shanghai, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
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8
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Yu Y, Zhang N, Mai Y, Ren L, Chen Q, Cao Z, Chen Q, Liu Y, Hou W, Yang J, Hong H, Xu J, Tong W, Dong L, Shi L, Fang X, Zheng Y. Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method. Genome Biol 2023; 24:201. [PMID: 37674217 PMCID: PMC10483871 DOI: 10.1186/s13059-023-03047-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/18/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Batch effects are notoriously common technical variations in multiomics data and may result in misleading outcomes if uncorrected or over-corrected. A plethora of batch-effect correction algorithms are proposed to facilitate data integration. However, their respective advantages and limitations are not adequately assessed in terms of omics types, the performance metrics, and the application scenarios. RESULTS As part of the Quartet Project for quality control and data integration of multiomics profiling, we comprehensively assess the performance of seven batch effect correction algorithms based on different performance metrics of clinical relevance, i.e., the accuracy of identifying differentially expressed features, the robustness of predictive models, and the ability of accurately clustering cross-batch samples into their own donors. The ratio-based method, i.e., by scaling absolute feature values of study samples relative to those of concurrently profiled reference material(s), is found to be much more effective and broadly applicable than others, especially when batch effects are completely confounded with biological factors of study interests. We further provide practical guidelines for implementing the ratio based approach in increasingly large-scale multiomics studies. CONCLUSIONS Multiomics measurements are prone to batch effects, which can be effectively corrected using ratio-based scaling of the multiomics data. Our study lays the foundation for eliminating batch effects at a ratio scale.
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Affiliation(s)
- Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yuanbang Mai
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qiaochu Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zehui Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, Guangdong, China
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | | | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
- International Human Phenome Institutes, Shanghai, China.
| | - Xiang Fang
- National Institute of Metrology, Beijing, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
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