Projects

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.

Overcoming treatment resistance conferred by intratumor heterogeneity

Colorectal cancer (CRC) is a leading cause of cancer-related deaths. Despite improvements in treatment, patients with metastatic disease relapse and have poor survival. A major contributor to therapeutic resistance is the presence of diverse phenotypes among cancer cell sub-populations, that is intratumoral heterogeneity (ITH).

Delineating cancer metastasis and drug resistance mechanisms using novel NGS technologies and organoid models