Ting Zhai

Postdoctoral Researcher at Stanford University

Department of Genetics, Stanford University

I am a Postdoctoral Researcher in the Snyder Lab at the Department of Genetics, Stanford University, working with Dr. Michael Snyder. My research focuses on biomarkers and lifestyle interventions that promote healthy longevity, integrating multi-omics data with lifecourse epidemiology to uncover actionable targets for aging and disease prevention.

PhD Research: I completed my Ph.D. in Population Health Sciences at Harvard University, advised by Drs. Zachary Nagel and David Christiani. My doctoral work centered on genome integrity and precision health — combining functional DNA repair assays, telomere biology, and multi-omics with longitudinal cohort data and causal inference methods to develop molecular biomarkers for cancer susceptibility and therapy response.

Previously, I earned my M.S. in Epidemiology at Harvard T.H. Chan School of Public Health studying pulmonary function as a predictor of survival in lung cancer patients, and my MBBS in Preventive Medicine from Qingdao University.

selected publications

MSIanalyzer: Targeted Nanopore Sequencing Enables Single Nucleotide Resolution Analysis of Microsatellite Instability Diversity

Ting Zhai, Ana Cheong, Daniel J. Laverty, and Zachary D. Nagel

Journal of Molecular Biology, 2026

Abs DOI

We present a targeted sequencing-based pipeline that profiles microsatellite instability (MSI) at single-nucleotide resolution. Targeted amplicons from the five widely studied Bethesda panel microsatellite loci were sequenced using Oxford Nanopore Technology in two microsatellite unstable colorectal cancer cell lines (HCT15, HCT116), two microsatellite stable cancer cell lines (TK6, U2OS), and two peripheral blood mononuclear cell samples from healthy donors. An anchor-extension algorithm was developed to capture repeat motifs while allowing interruptions, using a threshold informed by platform-specific error. Cluster-aware Dirichlet-multinomial and beta-binomial tests were applied for between-sample comparisons while accounting for read-level clustering within samples. The algorithm revealed distinct repeat profiles in HCT15 and HCT116 compared to other cell types and uncovered allelic diversity across samples at different MSI loci. Our approach complements existing short tandem repeat callers by preserving read-level diversity and delivering targeted, quantitative MSI calls with potential applications in mechanistic research and clinical assay development.
Telomere Length Dynamics As a Biomarker of Individual Radiation Sensitivity and Pneumonitis in Lung Cancer Patients Receiving Thoracic Radiotherapy

Ting Zhai, Sneh M. Toprani, Maeve Dillon-Martin, Patrick F. Doyle, Heejoo Kang, Claire Novack, Liming Liang, David C. Christiani, David E. Kozono, and Zachary D. Nagel

International Journal of Radiation Oncology*Biology*Physics, 2026

DOI
Comprehensive Measurement of Inter-Individual Variation in DNA Repair Capacity in Healthy Individuals

Ting Zhai, Patrizia Mazzucato, Catherine Ricciardi, David C. Christiani, Liming Liang, Leona D. Samson, Isaac A. Chaim, and Zachary D. Nagel

Advanced Science, 2025

Abs DOI

Rare genetic DNA repair deficiency syndromes can lead to immunodeficiency, neurological disorders, and cancer. In the general population, inter-individual variation in DNA repair capacity (DRC) influences susceptibility to cancer and several age-related diseases. Genome wide association studies and functional analyses show that defects in multiple DNA repair pathways jointly increase disease risk, but previous technologies did not permit comprehensive analyses of DNA repair in populations. To overcome these limitations, we used fluorescence multiplex host cell reactivation (FM-HCR) assays that directly quantify DRC across six major DNA repair pathways. We assessed DRC in phytohemagglutinin-stimulated primary lymphocytes from 56 healthy individuals and validated assay reproducibility in 10 individuals with up to five independent blood draws. We furthermore developed generalized analytical pipelines for systematically adjusting for batch effects and both experimental and biological confounders. Our results reveal significant inter-individual variation in DRC for each of 10 reporter assays that measure the efficiency of distinct repair processes. Our data also demonstrate that correlations between the activities of different DNA repair pathways are relatively weak. This finding suggests that each pathway may independently influence susceptibility to the health effects of DNA damage. We furthermore developed a pipeline for analyzing comet repair kinetics and related our new functional data to previously reported comet assay data for the same individuals. Our pioneering analysis underscores the sensitivity of FM-HCR assays for detecting subtle biological differences between individuals and establishes standardized methodologies for population studies. Our findings and open source analytical tools advance precision medicine by enabling comprehensive exploration of genetic, demographic, clinical, and lifestyle factors and supporting targeted interventions to enhance DNA repair and maintain genomic integrity, thereby promoting personalized healthcare and disease prevention.