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A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples
Open accessPublished version of a preprint
Abstract
Comparing diverse single-cell RNA sequencing (scRNA-seq) datasets generated by different technologies and in different laboratories remains a major challenge. Here we address the need for guidance in choosing algorithms leading to accurate biological interpretations of varied data types acquired with different platforms. Using two well-characterized cellular reference samples (breast cancer cells and B cells), captured either separately or in mixtures, we compared different scRNA-seq platforms and several preprocessing, normalization and batch-effect correction methods at multiple centers. Although preprocessing and normalization contributed to variability in gene detection and cell classification, batch-effect correction was by far the most important factor in correctly classifying the cells. Moreover, scRNA-seq dataset characteristics (for example, sample and cellular heterogeneity and platform used) were critical in determining the optimal bioinformatic method. However, reproducibility across centers and platforms was high when appropriate bioinformatic methods were applied. Our findings offer practical guidance for optimizing platform and software selection when designing an scRNA-seq study.
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“Recent benchmark studies indicate that for simpler integration problems with relatively low biological complexity and relatively small batch effects in scRNA-Seq datasets, linear methods outperform nonlinear, more complex methods136,137, while for complicated integration tasks with large biological complexity and bigger batch effects, nonlinear methods such as scVI/scanVI outperform others138.”
From A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain (2023) · cites this paper as [136]
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Comprehensive Integration of Single-Cell Data
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Benchmarking atlas-level data integration in single-cell genomics
Luecken, M. D., Büttner, M., Chaichoompu, K., Danese, A., Interlandi, M., Mueller, M. F., Strobl, D. C., Zappia, L., Dugas, M., Colomé-Tatché, M., et al. (2022) · Nature Methods · doi:10.1038/s41592-021-01336-8 · Cited by 1,438
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
Yao, Z., van Velthoven, C. T. J., Kunst, M., Zhang, M., McMillen, D., Lee, C., Jung, W., Goldy, J., Abdelhak, A., Aitken, M., et al. (2023) · Nature · doi:10.1038/s41586-023-06812-z · Cited by 1,203
Statistics or biology: the zero-inflation controversy about scRNA-seq data
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Self-citationTietscher, S., Wagner, J., Anzeneder, T., Langwieder, C., Rees, M., Sobottka, B., de Souza, N., & Bodenmiller, B. (2023) · Nature Communications · doi:10.1038/s41467-022-35238-w · Cited by 233
Assessing and mitigating batch effects in large-scale omics studies
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Metadata
- Authors
- Chen, W., Zhao, Y., Chen, X., Yang, Z., Xu, X., Bi, Y., Chen, V., Li, J., Choi, H., Ernest, B., Tran, B., Mehta, M., Kumar, P., Farmer, A., Mir, A., Mehra, U. A., Li, J.-L., Moos, M., Xiao, W., & Wang, C.
- Affiliations
- Loma Linda University (US)
- Frederick National Laboratory for Cancer Research (US)
- National Institute of Environmental Health Sciences (US)
- AbbVie (United States) (US)
- Takara (United States) (US)
- Center for Biologics Evaluation and Research (US)
- United States Food and Drug Administration (US)
- Corresponding author
- Xiao, Wenming
- Wang, Charles
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2020-12-21
- Volume
- 39
- Issue
- 9
- Pages
- 1103-1114
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC11245320
- OpenAlex
- W3117537317
- Cited by
- 114
- References
- 55
- Citations by year
- 2026: 21 · 2025: 15 · 2024: 16 · 2023: 21 · 2022: 21 · 2021: 19
- FWCI
- 4.93
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. Department of Health & Human Services | NIH | NIH Office of the Director (S10OD019960)
- Dr. Charles A. Sims’ gift to LLU Center for Genomics
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- single-cell RNA sequencing, benchmarking, reference samples, breast cancer cells, B cells, batch effect correction, normalization methods, preprocessing pipeline, cell classification, gene detection, platform comparison, cellular heterogeneity
- MeSH terms
- Algorithms, B-Lymphocytes, Breast Neoplasms, Female, Humans, Sequence Analysis, RNA, Benchmarking, Gene Expression Profiling, Cell Line, Tumor, Single-Cell Analysis, Datasets as Topic
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