Epidemiology & Biostatistics
The Ronglai Shen Lab
My research has focused on the development of novel statistical and bioinformatic methodologies that facilitate the study of translational research questions in cancer genomics and immuno-oncology. I developed several algorithms including iCluster and FACETS that are widely used in research community. My current research program focuses on two branches. First, in collaboration with Colin Begg, we are investigating the information content from rare somatic variants in the cancer genome toward identifying the primary for cancers detected via ctDNA or for cancers of unknown primary. Our group developed methods that made use of concepts developed in ecology and natural language processing to mine these rare signals across the whole genome for tracing the cancer site of origin. We are further extending these methods to identify somatic-germline associations in population-scale genome sequencing studies. In the second research branch, with a close collaboration with Margaret Callahan, a melanoma medical oncologist, we are mining multimodal datasets including flow cytometry, CITE-seq, multiplexed immunofluorescent imaging, and spatial transcriptomics to study diverse immune cell types in patient blood and tissue samples that predicts treatment response to immunotherapy. Our recent work led to the discovery of a blood-based LAG+ immunotype as an underlying mechanism of treatment resistance to anti-PD-1 therapy. Using a topic model, we linked this immunotype with an exhaustion phenotype that lacks immune-activation upon treatment using patient samples collected from a recent clinical trial. We are employing multi-modal single cell sequencing techniques to further characterize the LAG+ cells and spatial imaging technologies to study the characteristics of the tumor microenvironment.
Peng X, Lee J, Adamow M, Maher C, Postow MA, Callahan MK, Panageas KS, Shen R*. A topic modeling approach reveals the dynamic T cell composition of peripheral blood during cancer immunotherapy. Cell Reports Methods. 2023
Shen R, Postow MA, Adamow M, Arora A, Hannum M, Maher C, Wong P, Curran MA, Hollmann TJ, Jia L, Al-Ahmadie H, et al. LAG-3 expression on peripheral blood cells identifies patients with poorer outcomes after immune checkpoint blockade. Science translational medicine. 2021
Chakraborty S, Martin A, Guan Z, Begg C, Shen R*. Mining mutation contexts across the cancer genome to map tumor site of origin. Nat Communications. 2021
Shen R and Seshan V. (2016) FACETS: allele-specific copy number estimates from tumor sequencing. Nucleic Acids Res. 2016
Mo Q, Wang S, Seshan VE, Olshen AB, Schultz N, Sander C, Powers RS, Ladanyi M, and Shen R*. Pattern discovery and cancer gene identification in integrated cancer genomic data. Proc Natl Acad Sci U S A. 2013
Ronglai Shen, PhD
- My research has focused on the development of novel statistical and bioinformatic methodologies that facilitate the study of translational research questions in cancer genomics and immuno-oncology.
- PhD, University of Michigan, Ann Arbor, MI
- [email protected]
- Email Address