A Singular View of the Genome: Making Tools that Work

Thursday, November 11, 2010 - 11:00am - 12:00pm EST

  • Location:Jacobs Adminstrative Building, 5th Floor, Silleck Lounge
    Six MetroTech Center, Brooklyn, NY

David Schwartz
Vilas Professor of Chemistry and Genetics
University of Wisconsin-Madison

 

Abstract

Technological advances broaden our understanding of genomes, and new approaches employing single molecule analytes offer unique advantages for the discovery and characterization of genomic alterations complementing discernment of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs). CNVs commonly represent genomic events, such as amplifications and deletions usually found by DNA hybridization. Although such measures of genomic alteration are relatively comprehensive and have characterized small populations, CNVs effectively flag broad classes of genomic alterations, but do not readily discern genomic structural alterations embodied as translocations, gene-fusion events, amplifications, insertions, or rearrangements--both large and small scale (sub-genic). Furthermore, next-generation sequencing also offers limited structural insights, due to short read lengths, which attenuate genome coverage and discernment of complex events.

The Optical Mapping System, the first genomics platform to utilize single molecule analytes, exploits the detection range afforded by restriction fragment length polymorphism analysis, but with high throughput and single-DNA molecule precision engendered by automated fluorescence microscopy. Optical mapping enables the construction of genome-wide physical maps (consensus maps) from ensembles of ordered, single-DNA molecule restriction maps developed from genomic sources, obviating clone libraries, PCR, and hybridization. Comparisons of optical consensus maps against a reference map reveals structural alterations as “differences,” in the form of novel restriction sites (missing or extra cuts; MCs or ECs), or indels (insertions or deletions), which are statistically assessed, in part, based on the number of single-DNA molecule optical maps collectively represented by the consensus map. Since high-resolution restriction maps intrinsically reveal genome structure, elusive differences such as indels are discoverable and physically characterized.
 
In this talk, I will describe the workings of the Optical Mapping System, single molecule sequencing approaches, and present numerous applications covering normal and cancer genomes.

Refreshments will be served.