We welcome our next speaker in our seminar series, Dr. Charles Gawad from Stanford University where he is a Clinical Instructor in Pediatric Hematology and Oncology. He will be providing his seminar virtually via Zoom.
Studying Cellular Evolution with Primary Template-Directed Amplification
Abstract: Improvements in whole genome amplification (WGA) would enable new types of basic and applied biomedical research, including studies that require more accurate single-cell genotyping. In this lecture, I will present the development of primary template-directed amplification (PTA), an easily executed isothermal WGA method that limits the copying of daughter amplicons. This results in the reproducible production of shorter amplicons that cover almost the entire template genome in a uniform manner, resulting in much more accurate single-cell variant calling. In addition, the short amplicons produced by PTA allow for the incorporation of cell barcodes into the products, which we are utilizing to deploy PTA in highly parallel reactions using droplet-based microfluidics. Finally, I will discuss the numerous potential applications of PTA, including our initial studies showing that we can measure genome-environment interactions, off-target genome editing, cancer clonal evolution, and microbial diversity, all at cellular resolution.
Bio: Charles Gawad is a faculty member in the Department of Pediatrics at Stanford University and Chan Zuckerberg Biohub Investigator. He completed his undergraduate degree at Arizona State University and medical degree at the University of Arizona. He then underwent clinical training in pediatrics and pediatric hematology-oncology, during which he completed his PhD in Cancer Biology at Stanford where they unexpectedly found circular RNA is an abundant new class of noncoding RNA. Chuck then completed postdoctoral training in Stephen Quake’s group where they developed novel strategies for determining the evolutionary histories of cancers using single-cell genomics. As an independent scientist, he has continued to apply single-cell RNA and cell-free DNA sequencing to address scientific questions that have potential clinical significance. This has included creating a cell atlas of the developing mouse cerebellum as a foundation for more deeply understanding pediatric brain tumor formation, delineating the steps required for reprogramming cochlear supporting cells into inner ear hair cells to restore hearing, developing a strategy for predicting impending infections in cancer patients using cell-free DNA sequencing, and understanding the mechanisms of anti-tumor activity in autophagy-deficient macrophages. In addition, he has continued to develop single-cell DNA sequencing methods, including the invention of a new single-cell whole genome amplification method, primary template-directed amplification (PTA), which significantly outperforms all existing WGA methods for single-cell variant calling. Chuck’s work has been recognized with several awards, including an NIH Director’s New Innovator Award and Burroughs Wellcome Fund Career Award for Medical Scientists.