[PAST EVENT] Applied Science Seminar: Sean Koebley, Ph.D.
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Title: Nanomapping the genome: high-speed atomic force microscopy for translational biomedical research
Speaker: Sean R. Koebley, NIH IRACDA Postdoctoral Fellow, Physics Department, Virginia Commonwealth University
Abstract: Next-generation sequencing (NGS) has revolutionized biomedical research: as costs to sequence the whole human genome have fallen to near $1000, historic gains have been made in the study of genetic variants, diversity, transcription, and a range of other fields. However, NGS has yet to be effectively transferred to the clinical sphere, as its per-patient cost, time to construct an assembly (?1 week), and short-read limitations make it difficult to scale. Our lab has developed an alternative to NGS with the potential to bring the genomic age to patient care: a high-speed atomic force microscopy (HS-AFM) platform capable of ?nanomapping? the human genome. Our HS-AFM, the fastest atomic force microscope ever developed, produces a three-dimensional image of a 1 ?m2 surface with 1 nm resolution in less than 1 second. This combination of speed and accuracy allows targeted DNA fragments to be read with 15 bp resolution and tremendous statistical power, enabling the detection of pathogenic insertions or deletions. Additionally, we have developed the use of nuclease-inhibited CRISPR/Casa9 as a programmable nanoparticle. By targeting the nuclease-inhibited Cas9 molecule to a repeating sequence or set of sequences, a genetic ?barcode? is obtained in HS-AFM images that is compared to a reference to reveal the presence of genetic variants. Our approach can be applied as a programmable assay tuned to any hotspot of genetic mutation, and we are pursuing a shotgun-based method by which the entire exome or even genome could be probed via nanomapping. Sample preparation for our technique is simple and cost-negligible, data processing is conducted in near real-time, and we have shown that the most expensive component of our HS-AFM?its optical unit?can be replaced by a commercial DVD optical pickup. Thus, at a fraction of the cost and time of NGS and other comparable techniques, HS-AFM nanomapping has the potential to serve as a viable, scalable tool for the assessment of genetic disease in the clinical realm.