Cas9 targeted enrichment for nanopore profiling of methylation at known cancer drivers
About Timothy Gilpatrick
Timothy Gilpatrick is a current MD/PhD student at Johns Hopkins University working in the lab of Winston Timp to leverage sequencing technologies for insight into epigenetic states and transcriptional regulation. He received his BSc in Biochemistry from the University of Delaware, where he worked on characterizing the role of lipoprotein-associated enzymes in atherosclerosis. Prior to starting his graduate studies, he worked as a research fellow at the National Institutes of Health, where his work centered on understanding how microRNAs regulate epigenetic silencing machinery in mouse ES cells. He hopes to marry his interests in medicine and genomics to work in the development and application of sequencing-based diagnostic techniques. When not in lab, Timothy enjoys city biking, yoga, and music production.
CpG methylation in the mammalian genome is known to alter the binding of transcriptional regulatory factors, and through this activity mediate changes in chromatin structure and gene expression. We have previously shown the ability to call the methylation status of CpG sites using the signal from nanopore sequencing, and we are aiming to leverage this to profile the methylation status at high sequencing depth of genes known to be involved in tumorigenesis. These efforts have focused on using Cas9-enrichment, sidestepping the relatively high cost/bp of nanopore sequencing while retaining its exquisite sensitivity and long-reads. This allows us to profile signals of methylation over a long range on a single DNA molecule, and by comparing cells with different malignant potential, we can provide new insight into the dynamics of CpG methylation patterns. Specifically, we have targeted the promoter region of the human telomerase gene (hTERT), which is known to have altered methylation patterns that reflect the malignant potential of different cell line. This region is typically difficult to profile with bisulfite amplicon sequencing because of the repetitive and high CG density. Using thyroid cancer cell lines, we have sequenced this region, and identified both methylation level and individual single-read methylation patterns in the samples.