UC Santa Cruz

Degraded DNA isolated from diverse samples like ancient bones, environmental samples, forensic specimens and from blood plasma hold a wealth of information. However, due to the quality and quantity of the DNA isolated from these samples render them difficult to analyze using shotgun sequencing. Enrichment of the target regions of interest instead of sequencing the entire DNA is a cost-effective method. However, DNA/RNA baits need to enrich the target regions are expensive. In this thesis, I present a method for cost-effective DNA bait synthesis that I named as Circular Nucleic acid Enrichment Reagent (CNER, pronounced as snare) synthesis method. I demonstrate the application of the CNER method to make probes for specific target regions and for whole-genome enrichment (WGE). First, I use the CNER method to make probes for targeted genotyping of ~23k SNPs in the horse genome, using which I studied the demographic history of Late Pleistocene horses. Next, I demonstrate the CNER method to make WGE probes to detect and enrich entire genomes of Tuberculosis causing bacteria and Toxoplasmosis causing parasite. Finally, I demonstrate the CNER method to generate probes to enrich ~108k SNP markers for genotyping DNA isolated from rootless hair for forensic application.