ArticleNature biotechnology2024
Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling.
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Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 23 papers.
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23citing papers in PubMed
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23 citing papers in PubMed.
- Ensuring multiomics data reproducibility for artificial intelligence with reference materials as a common calibrator.Nature biotechnology · 2026Article
- Distinct multi-omics signatures of clinical subgroups of type 2 diabetes define heterogeneous responses to an insulin sensitizer.Nature communications · 2026Article
- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- Benchmarking Q40 sequencing for sensitive and efficient detection of rare genomic variants.Genome biology · 2026Article
- Multi-omics biomarkers in endometrial receptivity: from mechanisms to clinical translation.Journal of translational medicine · 2026Review
- A metrological foundation for absolute transcriptomics using International System of Units-anchored calibrators.Nature communications · 2026Article
- A self-adaptive and versatile tool for eliminating multiple undesirable variations from large-scale transcriptomes.Nature biomedical engineering · 2026Article
- New insight into RNA biomarkers in neuropathic pain: a clinician-neuroscientist roadmap to translational testing and treatment monitoring a clinical review.Frontiers in pain research (Lausanne, Switzerland) · 2026Review
- The Influence of Sleep and Diet on Human Peripheral Immunity and Chronic Health Conditions.Research (Washington, D.C.) · 2026Article
- Metagenomic Data Preprocessing and Quality Control.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Genomic and transcriptomic dynamics in the stepwise progression of lung adenocarcinoma.Cell research · 2025Article
- Protein-level batch-effect correction enhances robustness in MS-based proteomics.Nature communications · 2025Article
- Methylation reference datasets from quartet DNA materials for benchmarking epigenome sequencing.Nature communications · 2025Article
- The important role of standards for the uptake of transcriptomics and metabolomics based in vitro methods in regulatory toxicology.Archives of toxicology · 2025Review
- Construction of RNA reference materials for improving the quantification of transcriptomic data.Nature protocols · 2025Review
- Multi-omics Quality Assessment in Personalized Medicine Through European Infrastructure for Translational Medicine (EATRIS): An Overview.Phenomics (Cham, Switzerland) · 2025Review
- Establishment of potential reference measurement procedure and reference materials for EML4-ALK fusion variants measurement.Scientific reports · 2024Article
- Assessing and mitigating batch effects in large-scale omics studies.Genome biology · 2024Review
- A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials.Nature communications · 2024Article
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials.Nature biotechnology · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
49 authors.
Ying Yu *State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-4084-908X
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.ORCID http://orcid.org/0000-0001-9356-9164
Haiyan Wang *State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Lianhua Dong *National Institute of Metrology, Beijing, China.
Yuanbang MaiState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Qingwang ChenState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-7191-5801
Zhihui LiState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Shanyue SunState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Jingcheng YangState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Zehui CaoState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Peipei ZhangState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Yi ZiState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Ruimei LiuState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Jian GaoState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Naixin ZhangState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Jingjing LiState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-0142-5495
Luyao RenState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
He JiangState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0003-0673-0605
Jun ShangState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-5767-1492
Sibo ZhuState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Xiaolin WangState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Tao QingState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Ding BaoState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Bingying LiState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Bin LiState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Chen SuoState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Yan PiState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
Xia WangNational Institute of Metrology, Beijing, China.
Fangping DaiGenome Decoding Institute, Nantong, China.
Andreas SchererInstitute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.ORCID http://orcid.org/0000-0002-4254-7122
Pirkko MattilaInstitute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
Jinxiong HanNanjing Vazyme Biotech Co. Ltd., Nanjing, China.
Lijun ZhangNanjing Vazyme Biotech Co. Ltd., Nanjing, China.
Hui JiangMGI, BGI-Shenzhen, Shenzhen, China.
Danielle Thierry-MiegNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0001-9568-4211
Jean Thierry-MiegNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-0396-6789
Wenming XiaoOffice of Oncologic Diseases, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA.ORCID http://orcid.org/0000-0003-4096-9724
Huixiao HongDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.ORCID http://orcid.org/0000-0001-8087-3968
Weida TongDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.ORCID http://orcid.org/0000-0003-3488-6148
Jing WangNational Institute of Metrology, Beijing, China.
Jinming LiNational Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China.
Xiang FangNational Institute of Metrology, Beijing, China.
Li JinState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0001-9201-2321
Joshua XuDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA. joshua.xu@fda.hhs.gov.ORCID http://orcid.org/0000-0001-5313-5847
Feng QianState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China. fengqian@fudan.edu.cn.ORCID http://orcid.org/0000-0002-2312-5936
Rui ZhangNational Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China. ruizhang@nccl.org.cn.ORCID http://orcid.org/0000-0003-4660-2042
Leming ShiState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China. lemingshi@fudan.edu.cn.ORCID http://orcid.org/0000-0002-2981-4150
Yuanting ZhengState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China. zhengyuanting@fudan.edu.cn.ORCID http://orcid.org/0000-0003-4480-8303
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Gene Expression ProfilingReference StandardsTranscriptomeCell LineHumansQuality ControlReproducibility of ResultsRNASequence Analysis, RNATwins, MonozygoticRNA
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