ALBUQUERQUE, N.M. — Sandia National Laboratories and the University of New Mexico have produced better scanning technology by developing a new kind of scanner called a hyperspectral imager.
Sandia researcher David Haaland says the scientists found many problems with the existing microarray scanner technology, including a need for greater sensitivity for low-expressed genes and the fact that comparisons between microarray experiments are limited due to poor reproducibility.
“But our main issue was slide fluorescence from impurities,” he says. “The slides had spectral interferences that resulted in extraneous light causing loss of quantitative accuracy.”
Haaland needed a device that would eliminate the influences of the impurities and provide much more accurate data that could be fed into the computers for analysis. He turned to fellow Sandian Mike Sinclair, known for co-inventing the Polychromator that uses a combination of optics and microelectromechanical systems (MEMS) to determine gas types.
“David talked to me a long time, wondering if some aspect of the Polychromator could be used to solve this problem,” Sinclair says. “The answer was no. But I thought I could build a machine that could do the job.”
After analyzing several approaches to array scanning, he developed a design and built the Hyperspectral Microarray Scanner for Microarray Analysis primarily from commercial parts.
The scanner he developed is potentially more sensitive than any commercial microarray scanners. Among some of its advantages: considerably greater accuracy and improved rejection of stray light and impurity emission.
Sinclair started the design of the new scanner in April of last year and by late November he, with the help of Jeri Timlin and Gary Jones at Sandia, had a working device that was providing almost pure data from the slides provided by UNM biology professor Maggie Werner-Washburne and the UNM Cancer Research and Treatment Center.
He can put what appears to be a clean slide with only the DNA samples in the hyperspectral microarray scanner, and after illuminating it with one or more lasers, see several impurities in the slide.
“I built this machine, but it is still amazing to use it and see all this information pop out on what looked like a clear glass slide,” Sinclair says.
The hyperspectral microarray scanner provides Sinclair with huge data files that they put on CDs. Haaland, Timlin and George Davidson then perform the analysis using Sandia-developed algorithms and software.
The new scanner uses proprietary multivariate software developed in other hyperspectral image analysis projects at Sandia. The result is that they can determine pure-component fluorescence spectra and DNA concentrations in each spot without the use of standards.
Sinclair will soon be building a second, improved hyperspectral microarray scanner that will be used to study a seaborne bacteria, Synechococcus, as part of the recently announced Department of Energy “Genomes to Life” project.
University of New Mexico Contact: Steve Carr, scarr@unm.edu, (505) 277-1821