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Outsourced Sequencing, Field Programmable Gate Arrays, Tissue Arrays, and Proteomics in the Clinic

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The March 2004 cover story of Genome Technology focused on a new trend in DNA sequencing: outsourcing. To get the throughput needed for their projects, some researchers began to turn to companies rather than to their institutions' core labs. Since then, next-generation sequencing has exploded onto the scene, bringing even higher throughput with it — and outsourcing is still going strong. At the time of the article, Lark Technologies had just been acquired by Genaissance which was, in turn, bought by Clinical Data in June 2005. Clinical Data's genomics services division, Cogenics, now offers sequencing on its Applied Biosystems 3730XL/DNA Analyzer as well as with Roche's 454 FLX. Since 2004, MWG Biotech merged with Operon Biotechnologies and Medigenomix to become Eurofins MWG Operon; the resulting company also offers both Sanger and next-gen sequencing services.

That same year, an article profiled the work of RIKEN's Yoshiki Yamaguchi. Yamaguchi and his colleagues Tsutomu Maruyama and Akihiko Konagaya tinkered with a Pentium-based PC, adding a field programmable gate array, to be able to do high-speed homology searches on a desktop without breaking the bank. Yamaguchi and Maruyama are now at the University of Tsukuba in Japan, and Konagaya is a visiting professor at the Tokyo Institute of Technology. The three recently presented at the International Conference on Field Programmable Logic and Applications on using FPGA and the Carrillo-Lippman method to find optimal sequence alignments quickly.

A feature story in last year's issue looked into the role of tissue arrays and their problems with imaging and standardization. One way around the issue is to measure absolute protein concentrations as HistoRx's Aqua platform does. The platform was licensed last May to the Dana-Farber/Harvard Cancer Center for use in cancer biomarker profiling studies. Also, Eli Lilly has extended and expanded its 2005 agreement with HistoRx, and the Aqua platform will be used in Lilly's pharmaceutical development programs.

Another story in last year's GT focused on the role proteomics can play in the clinic, particularly to detect diseases early on. Since then, protein biomarkers continue to make a splash. Expression Pathology and the Alberta Cancer Board's Tom Baker Cancer Centre have announced they are looking to identify protein biomarkers that presage breast cancer metastasis, and David Wong at the University of California, Los Angeles, is developing a method to detect protein biomarkers for oral cancer in saliva.

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