Chapter 9 A Single Molecule System for Whole Genome Analysis

Abstract Optical mapping is a fully automated single molecule system for creating ordered restriction maps directly from genomic DNA molecules. The system has integrated components drawn from chemistry, physics, genetics, computer science, statistics, and engineering allowing whole genome analysis through analysis of large collections of individual DNA molecules. Such large-scale analysis is potentiated by analytes consisting of high molecular weight genomic DNA molecules that are arrayed using microfluidic devices; this step fosters high-throughput acquisition of image data. DNA “barcodes” are created using the action of restriction endonucleases on arrayed molecules from the analysis of images acquired by automated microscopy embedded within an integrated system. This system links together machine vision, barcode assembly and comparative analysis software with the massive computational power of cluster computing. After assembly of these barcodes into genome-wide physical maps, complex genome structure is revealed, characterizing genomic alterations, in addition to providing scaffolds for genome sequence assembly, or validation. Further sequence information is obtainable from barcoded DNA molecules using optical sequencing technology, delivering strings of nucleotide data from barcoded loci.