This article discusses the use of a novel method for cost-effective DNA bait synthesis and demonstrates its applicability for targeted genotyping, making whole-genome enrichment probes, and generating probes for the genotyping of DNA isolated from rootless hair for forensic purposes.
Degraded DNA isolated from diverse samples like ancient bones, environmental samples, forensic specimens and from blood plasma hold a wealth of information. However, 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, the author presents a method for cost-effective DNA bait synthesis that the author named Circular Nucleic acid Enrichment Reagent (CNER, pronounced as snare) synthesis method. In this article, the author demonstrates the application of the CNER method to make probes for specific target regions and for whole-genome enrichment (WGE). First, the CNER method is used to make probes for targeted genotyping of ~23k SNPs in the horse genome, for the demographic history of Late Pleistocene horses. Next, the author demonstrates the CNER method to make WGE probes to detect and enrich entire genomes of Tuberculosis causing bacteria and Toxoplasmosis causing parasite. Finally, the CNER method is used to generate probes to enrich ~108k SNP markers for genotyping DNA isolated from rootless hair for forensic application. Publisher Abstract Provided