Projects
Integrating Quantitative Genomics and Spatial Architecture of Tumor-Infiltrating Lymphocytes
TILs are crucial in the tumor microenvironment, influencing survival and immunotherapy response, but their large-scale analysis is challenging. We developed a deep learning framework using molecular label transferring to automate TIL identification from histopathology images. Our project aims to quantify TILs, correlate them with tumor mutation burden, and assess their link to immune checkpoint blockade responses, enabling scalable and integrative cancer analysis.
Identifying Methylation Signatures of Cell free DNA for Early Detection
Distinct cell-free DNA (cfDNA) methylation and fragmentation patterns are identified in cerebrospinal fluid from NSCLC patients with brain metastases. Using nanopore sequencing, researchers found unique 5mC and 5hmC signatures, suggesting potential biomarkers for early detection.
Gastric Cancer Registry
In 2011, Gastric Cancer Foundation launched the first Gastric Cancer Registry, a secure HIPAA-compliant database at Stanford University. Registry researchers in the Ji Research Group gather comprehensive data about people with stomach cancer, including lifestyle, health and family histories, environmental factors as well as physical samples of the tumors themselves.
In order to conduct breakthrough research, we encourage all people with gastric cancer (or their families) to sign up with the registry. It’s an easy process that can make a world of difference.
Immunogenic neo-antigen discovery for personalized immuno therapy
Recent advances in cancer immunotherapy and genomic sequencing technologies have created promising opportunities for precision cancer medicine. Somatic coding mutation in cancer genomes may lead to amino acid alterations that generate immunogenic peptides, called neoantigens.
Intratumor Heterogeneity
Genome perspective: Several cancer types consist of multiple genetically distinct subpopulations. The underlying mechanism for this intra-tumor heterogeneity can be explained by the clonal evolution model, whereby growth advantageous mutations cause the expansion of cancer cell subclones.
Short Tandem Repeat Sequencing (STR-Seq)
Microsatellites, also referred to as short tandem repeats (STRs) are multiallelic in terms of germline variation and have higher mutation rate than single nucleotide polymorphisms (SNPs). Because of the highly polymorphic nature, microsatellites are the most popular and versatile genetic marker with many applications including forensics DNA fingerprinting and population genetics.
Linked Read Sequencing
Developing tools to extend the utility of the novel linked read sequencing technology for more applications.
Single-molecule resolution mutation detection using single-color droplet digital PCR from un-amplified circulating tumor DNA
Our novel single color digital droplet PCR (ddPCR) molecular assay can detect and quantifying cancer mutations directly from poor quality and limited quantity DNA samples such as un-amplified circulating tumor DNA (ctDNA) collected from the plasma of cancer patients.
Identifying targets and resistance mechanisms resulting from intra-tumor heterogeneity
Tumor cells are surrounded by a unique microenvironment. This heterogeneity enables tumors to grow and promotes resistance to treatment but can also serve as a source of novel targets.
