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Proceedings Paper

Technical approaches for efficient high-precision nucleic acid analysis using DNA microarrays
Author(s): Daniel Pinkel; Gregory Hamilton; Nils Brown; Richard Segraves; Bing Huey; Anoine Snijders; Stephanie Blackwood; Kate Hindle; Sindy Law; Joe W. Gray; Ajay Jain; John Hanson; Robert Nordmeyer; Donna Albertson
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Paper Abstract

Microarray measurements offer the potential to compare the abundances of numerous nucleic acid sequences in parallel. Using linker-adapter PCR products from mapped BAC clones we have made arrays that permit scanning the human genome for single copy gains and losses of DNA sequence, which requires reliable detection of 50 percent changes. The DNA is printed at high concentration on amino-silane or chromium coated surface using a custom-built capillary pin printing system. Spots are printed on 130 micrometers centers or closer to minimize the size of the arrays. Hybridization occurs in a dextran sulfate/formamide buffer at 37 degrees C, using slow rocking to mix the reaction. The entire array is imaged in a single CCD frame using a custom built system that employs mercury arc illumination. Up to four fluorochromes can be imaged from a single array with adequate spectral separation. Typically we use DAPI to stain the DNA in the array spots to facilitate automatic image segmentation during analysis, and fluorescein, Cy3, and Cy5 or their spectral equivalents, for labeling specimen nucleic acids. Array spots are segmented and quantitative fluorescence intensities and intensity ratios are automatically calculated in < 1 minute per approximately 8000 element array using the custom software UCSF SPOT.

Paper Details

Date Published: 21 June 2002
PDF: 7 pages
Proc. SPIE 4626, Biomedical Nanotechnology Architectures and Applications, (21 June 2002); doi: 10.1117/12.472067
Show Author Affiliations
Daniel Pinkel, Comprehensive Cancer Ctr./Univ. of California/San Francisco (United States)
Gregory Hamilton, Comprehensive Cancer Ctr./Univ. of California/San Francisco (United States)
Nils Brown, Comprehensive Cancer Ctr./Univ. of California/San Francisco (United States)
Richard Segraves, Comprehensive Cancer Ctr./Univ. of California/San Francisco (United States)
Bing Huey, Comprehensive Cancer Ctr./Univ. of California/San Francisco (United States)
Anoine Snijders, Comprehensive Cancer Ctr./Univ. of California/San Francisco (United States)
Stephanie Blackwood, Comprehensive Cancer Ctr./Univ. of California/San Francisco (United States)
Kate Hindle, Comprehensive Cancer Ctr./Univ. of California/San Francisco (United States)
Sindy Law, Comprehensive Cancer Ctr./Univ. of California/San Francisco (United States)
Joe W. Gray, Comprehensive Cancer Ctr./Univ. of California/San Francisco (United States)
Ajay Jain, Comprehensive Cancer Ctr./Univ. of California/San Francisco (United States)
John Hanson, Hanson Inc. (United States)
Robert Nordmeyer, Lawrence Berkeley National Lab. (United States)
Donna Albertson, Comprehensive Cancer Ctr./Univ. of California/San Francisco (United States)


Published in SPIE Proceedings Vol. 4626:
Biomedical Nanotechnology Architectures and Applications
Raymond P. Mariella; Catherine J. Murphy; Michelle Palmer; David A. Dunn; Darryl J. Bornhop; David A. Dunn; Raymond P. Mariella; Catherine J. Murphy; Dan V. Nicolau; Shuming Nie; Michelle Palmer; Ramesh Raghavachari; Darryl J. Bornhop; Ramesh Raghavachari; Shuming Nie; Ramesh Raghavachari, Editor(s)

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