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Optical Mapping with OpGen, Whole Genome Arrays, and Functional Genomics

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Five years ago in the October 2003 issue, Genome Technology featured OpGen, at the time a small Madison, Wis.-based startup founded on a promising optical mapping technology developed by David Schwartz. The story wondered whether the company could go head-to-head with sequencing companies to use its optical restriction mapping technique for whole genome analysis. In 2007, several years into providing an optical mapping service to the research community, the company raised $23.6 million and announced that it would discontinue service and shift its focus to developing a commercially available instrument for microbial identification in clinical settings. Due to high demand, however, it resumed service this April. With the hopes of using its maps and next-gen sequencing data for bacterial genome assemblies, OpGen plans to open a facility in Gaithersburg, Md.

The cover story in that same issue looked at the then-nascent market of whole genome arrays. At the time, Affymetrix, Agilent Technologies, Applied Biosystems, and NimbleGen all were about to introduce chips; customers, however, were leery about choosing the right platform for their needs. Five years down the road, of course, the field has skyrocketed. Affymetrix now offers gene chips not just for humans, but for Arabidopsis, dog, cow, maize, and cotton, among many others. Whole genome expression analysis is not the only application, with these arrays taking on genotyping, resequencing, array CGH, chromatin immunoprecipitation, and DNA methylation analysis. SNP arrays have reached the 1 million probe mark, with Affy's Human SNP Array 6.0 and Illumina's Human1M chip leading the industry. Analysts, however, are skeptical that ever-increasing density may soon be tempered with diminishing returns on data analysis.

A year ago, the cover story checked into functional genomics, surveying different areas of research and tools being used to match genes with function. BU's Jim Collins spoke about synthetic biology, one area where functional genomics has had a large impact. He created a genetic toggle switch in bacteria that, when combined with RNAi, could give 100 percent knockdown. Sudhir Kumar, director of the Center for Evolutionary Functional Genomics at Arizona State, launched a program called Molecular Evolutionary Genetics Analysis to help scientists study functional genomics. As researchers continue to tap microarrays, they're also eyeing new sequencing technologies to help them move from genes to proteins, harnessing powerful applications like ChIP-seq and transcriptome expression analysis.

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