Advances and applications in single-cell and spatial genomics

Jingjing Wang^#¹, Fang Ye^#¹, Haoxi Chai^#², Yujia Jiang^#^{3

4}, Teng Wang^#^{5

6}, Xia Ran^#^{1

7}, Qimin Xia^#⁵, Ziye Xu^#⁸, Yuting Fu^#^{1

9}, Guodong Zhang^#^{1

9}, Hanyu Wu^#^{1

9}, Guoji Guo^{10

11

12

13}, Hongshan Guo^{14

15}, Yijun Ruan¹⁶, Yongcheng Wang¹⁷, Dong Xing^{18

19}, Xun Xu^{20

21

22}, Zemin Zhang²³

Affiliations

¹ Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China.
² Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, 310058, China.
³ BGI Research, Shenzhen, 518083, China.
⁴ BGI Research, Hangzhou, 310030, China.
⁵ Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing, 100871, China.
⁶ Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
⁷ Institute of Hematology, Zhejiang University, Hangzhou, 310000, China.
⁸ Department of Laboratory Medicine of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China.
⁹ Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.
¹⁰ Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China. ggj@zju.edu.cn.
¹¹ Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China. ggj@zju.edu.cn.
¹² Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, 310058, China. ggj@zju.edu.cn.
¹³ Institute of Hematology, Zhejiang University, Hangzhou, 310000, China. ggj@zju.edu.cn.
¹⁴ Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China. guohs@zju.edu.cn.
¹⁵ Institute of Hematology, Zhejiang University, Hangzhou, 310000, China. guohs@zju.edu.cn.
¹⁶ Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, 310058, China. yjruan@zju.edu.cn.
¹⁷ Department of Laboratory Medicine of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China. yongcheng@zju.edu.cn.
¹⁸ Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing, 100871, China. dxing@pku.edu.cn.
¹⁹ Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, 100871, China. dxing@pku.edu.cn.
²⁰ BGI Research, Shenzhen, 518083, China. xuxun@genomics.cn.
²¹ BGI Research, Hangzhou, 310030, China. xuxun@genomics.cn.
²² Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China. xuxun@genomics.cn.
²³ Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing, 100871, China. zemin@pku.edu.cn.

^# Contributed equally.

PMID: 39792333
DOI: 10.1007/s11427-024-2770-x

Review

Advances and applications in single-cell and spatial genomics

Jingjing Wang et al. Sci China Life Sci. 2025 May.

. 2025 May;68(5):1226-1282.

doi: 10.1007/s11427-024-2770-x. Epub 2024 Dec 20.

Authors

Affiliations

¹ Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China.
² Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, 310058, China.
³ BGI Research, Shenzhen, 518083, China.
⁴ BGI Research, Hangzhou, 310030, China.
⁵ Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing, 100871, China.
⁶ Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
⁷ Institute of Hematology, Zhejiang University, Hangzhou, 310000, China.
⁸ Department of Laboratory Medicine of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China.
⁹ Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.
¹⁰ Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China. ggj@zju.edu.cn.
¹¹ Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China. ggj@zju.edu.cn.
¹² Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, 310058, China. ggj@zju.edu.cn.
¹³ Institute of Hematology, Zhejiang University, Hangzhou, 310000, China. ggj@zju.edu.cn.
¹⁴ Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China. guohs@zju.edu.cn.
¹⁵ Institute of Hematology, Zhejiang University, Hangzhou, 310000, China. guohs@zju.edu.cn.
¹⁶ Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, 310058, China. yjruan@zju.edu.cn.
¹⁷ Department of Laboratory Medicine of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 310058, China. yongcheng@zju.edu.cn.
¹⁸ Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing, 100871, China. dxing@pku.edu.cn.
¹⁹ Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, 100871, China. dxing@pku.edu.cn.
²⁰ BGI Research, Shenzhen, 518083, China. xuxun@genomics.cn.
²¹ BGI Research, Hangzhou, 310030, China. xuxun@genomics.cn.
²² Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China. xuxun@genomics.cn.
²³ Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing, 100871, China. zemin@pku.edu.cn.

^# Contributed equally.

PMID: 39792333
DOI: 10.1007/s11427-024-2770-x

Abstract

The applications of single-cell and spatial technologies in recent times have revolutionized the present understanding of cellular states and the cellular heterogeneity inherent in complex biological systems. These advancements offer unprecedented resolution in the examination of the functional genomics of individual cells and their spatial context within tissues. In this review, we have comprehensively discussed the historical development and recent progress in the field of single-cell and spatial genomics. We have reviewed the breakthroughs in single-cell multi-omics technologies, spatial genomics methods, and the computational strategies employed toward the analyses of single-cell atlas data. Furthermore, we have highlighted the advances made in constructing cellular atlases and their clinical applications, particularly in the context of disease. Finally, we have discussed the emerging trends, challenges, and opportunities in this rapidly evolving field.

Keywords: cell atlas; clinical application; multi-omics; single-cell; spatial; technologies.

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Conflict of interest statement

Compliance and ethics. The authors declare that they have no conflict of Interest.

References

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Advances and applications in single-cell and spatial genomics

Affiliations

Advances and applications in single-cell and spatial genomics

Authors

Affiliations

Abstract

Conflict of interest statement

References

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources