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Human Genome News, April-June 1996; 7(6)

Santa Fe '96

Stretched to the Max: FISH Mapping on DNA Fibers

A new technique based on applying FISH techniques to linear stretched DNA molecules may help researchers resolve issues critical to large-scale DNA sequencing efforts.

Heinz-Ulrich Weier (Resource for Molecular Cytogenetics) says the recently developed technique, called quantitative DNA fiber mapping (QDFM), can help researchers construct high-resolution physical maps and minimal tiling paths, assess gap sizes and devise closure strategies, and provide quality-control checks during map- and sequence-assembly steps.

QDFM combines molecular combing techniques to attach and stretch DNA molecules across a glass microscope slide. FISH is used to hybridize fluorescently tagged probes to the straightened DNA fibers. Digital image technology records and analyzes images from the fluorescence microscope and measures the position of the DNA sequence or probe along the DNA fiber.

QDFM is rapid and provides a high spatial resolution of 1 to 2 kb, up to 1 Mb. Throughput of QDFM could be increased dramatically with automated image analysis that includes algorithms for finding the fibers, autofocusing, and handling multiple slides.

With as many as 20 clones combed on a single microscope slide, early results look promising, but QDFM's impact on genome research will depend on how well it scales up. The technique is amenable to automation, notes Weier, which could increase its throughput manyfold. Berkeley Lab plans to integrate QDFM into the large-scale sequencing process. (Related article: http://publications.lbl.gov/fedora/repository/ir%3A125116; note article link added post-publication.)

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Human Genome Project 1990–2003

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