Alleviating batch effects in cell type deconvolution with SCCAF-D
Cell type deconvolution methods can impute cell proportions from bulk transcriptomics data, revealing changes in disease progression or organ development. But benchmarking studies often use simulated bulk data from the same source as the reference, which limits its application scenarios. This study examines batch effects in deconvolution and introduces SCCAF-D, a computational workflow that ensures a Pearson Correlation Coefficient above 0.75 across simulated and real bulk data for various tissue types. Applied to non-alcoholic fatty liver disease, SCCAF-D unveils meaningful insights into changes in cell proportions during disease progression.
Authors
- Irene Papatheodorou (ORCID: https://orcid.org/0000-0001-7270-5470)
- Anna Vathrakokoili Pournara (ORCID: https://orcid.org/0000-0002-2701-1987)
- Xinlu Yang
- Shuo Feng (ORCID: https://orcid.org/0000-0002-1739-6385)
- Zhichao Miao (ORCID: https://orcid.org/0000-0002-5777-9815)
- Ming Shi (ORCID: https://orcid.org/0000-0003-0527-0061)
- Alvis Brāzma (ORCID: https://orcid.org/0000-0001-5988-7409)
- Liangfeng Huang (ORCID: https://orcid.org/0000-0002-0977-9183)
- Ziliang Huang (ORCID: https://orcid.org/0000-0002-4102-3300)
- Yongjian Zhang (ORCID: https://orcid.org/0000-0002-4975-452X)
Institutions
- University of East Anglia (GB)
- Tongji University (CN)
- University of Science and Technology of China (CN)
- European Bioinformatics Institute (GB)
- Harbin Medical University (CN)
- Harbin Institute of Technology (CN)
- Norwich Research Park (GB)
- Earlham Institute (GB)
- Second Affiliated Hospital of Harbin Medical University (CN)
- Bioinformatics Institute (RU)
- Shanghai Center for Brain Science and Brain-Inspired Technology (CN)
- Guangzhou Medical University (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-12-30
- DOI
- https://doi.org/10.1038/s41467-024-55213-x
- Citations
- 4
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 0.94
Funders
- World Habitat
- National Natural Science Foundation of China
- Biotechnology and Biological Sciences Research Council