Zongli Zheng

Dr. Zongli Zheng was Assistant Professor at Ming Wai Lau Centre for Reparative Medicine between 2017 and 2023.

Photo of Zongli Zheng.


Dr. Zheng received his PhD degree in medical epidemiology from Karolinska Institutet in 2011 and completed a postdoctoral training at Massachusetts General Hospital and Harvard Medical School in 2015, with support from the Swedish Research Council International Postdoc Fellowship. 


Our contribution to precision medicine includes the invention of the AMP technology that enables gene fusion discovery and, following initial clinical implementations in top US hospitals (MSK Solid Fusion, MGH NGS Fusion, etc.), has now been adopted globally for robust clinical assays for gene fusion detection to guide targeted therapy for cancer patients. We have also developed the GUIDE-seq method that has become a reference for genome-wide unbiased profiling of CRISPR edits. Currently, we focus on:

  • Genome engineering – to characterize genome-wide CRISPR targeting profile and improve its genome editing precision for treating diseases rooted in altered DNA bases or chromosomal structure.
  • Single-cell genomics – to develop a scalable and integrated single-cell genomic characterization platform for functional screening and identification of therapeutic targets.

Group Members

Previous lab members

Qinle Zhang | Postdoctoral Researcher

Siyu Bao | Research Assistant

Athena Chu | Senior Research Assistant

Baifeng Zhang | Research Assistant

Chloe Bao | Research Assistant

Jinhuan Li | Postdoctoral Researcher

Limei Ai | Research Assistant

Evangeline Kang | Postdoctoral Researcher

Bang Wang | Postdoctoral Researcher

Silvia Mak | Research Assistant

Jan Keung | Research Officer

Miao Yu | Research Assistant

Maggie Chow | Research Officer

Yee Man Chan | Senior Bioinformatician

Furong Ju | Postdoctoral Researcher

Weiwei Bian | Senior Research Assistant

Shifeng Lian | Senior Research Assistant

Qian Luo | Senior Research Assistant

Jerry Gan | Research Assistant

Zihua Jiang | Research Assistant


Selected Publications

Full list: Google Scholar

Song Z, Lian S, Mak S, Chow ZY, Xu C, Wang W, Keung HY, Lu C, Kebede TF, Gao Y, Cheuk W, Cho CS, Yang M, Zheng Z. (2021). Deep RNA sequencing revealed fusion junctional heterogeneity may predict crizotinib treatment efficacy in ALK-rearranged non-small cell lung cancer. Journal of Thoracic Oncology, (ePub).

Song Z, Lu C, Xu C, Zheng Z. (2021). Noncanonical gene fusions detected at the DNA level necessitate orthogonal diagnosis methods before targeted therapy. Journal of Thoracic Oncology (2021) 16:344-348

Tan, Y., Chu, A. H. Y., Bao, S., Hoang, D. A., Kebede, F. T., Xiong, W., Ji, M., Shi, J., & Zheng, Z. (2019). Rationally engineered Staphylococcus aureus Cas9 nucleases with high genome-wide specificity. Proceedings of the National Academy of Sciences, 116(42), 20969–20976.

Choi, G. C. G., Zhou, P., Yuen, C. T. L., Chan, B. K. C., Xu, F., Bao, S., Chu, H. Y., Thean, D., Tan, K., Wong, K. H., Zheng, Z., & Wong, A. S. L. (2019). Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9. Nature Methods, 16(8), 722–730.

Kleinstiver, B. P., Pattanayak, V., Prew, M. S., Tsai, S. Q., Nguyen, N. T., Zheng, Z., & Joung, J. K. (2016). High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature, 529(7587), 490–495.

Kleinstiver, B. P., Prew, M. S., Tsai, S. Q., Nguyen, N. T., Topkar, V. V., Zheng, Z., & Joung, J. K. (2015). Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition. Nature Biotechnology, 33(12), 1293–1298.

Tsai, S. Q., Zheng, Z., Nguyen, N. T., Liebers, M., Topkar, V. V., Thapar, V., Wyvekens, N., Khayter, C., Iafrate, A. J., Le, L. P., Aryee, M. J., & Joung, J. K. (2015). GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nature Biotechnology, 33(2), 187–197.

Shaw, A. T., Ou, S.-H. I., Bang, Y.-J., Camidge, D. R., Solomon, B. J., Salgia, R., Riely, G. J., Varella-Garcia, M., Shapiro, G. I., Costa, D. B., Doebele, R. C., Le, L. P., Zheng, Z., Tan, W., Stephenson, P., Shreeve, S. M., Tye, L. M., Christensen, J. G., Wilner, K. D., … Iafrate, A. J. (2014). Crizotinib in ROS1 -Rearranged Non–Small-Cell Lung Cancer. New England Journal of Medicine, 371(21), 1963–1971.

Zheng, Z., Liebers, M., Zhelyazkova, B., Cao, Y., Panditi, D., Lynch, K. D., Chen, J., Robinson, H. E., Shim, H. S., Chmielecki, J., Pao, W., Engelman, J. A., Iafrate, A. J., & Le, L. P. (2014). Anchored multiplex PCR for targeted next-generation sequencing. Nature Medicine, 20(12), 1479–1484.

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