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Proceedings Paper

High-throughput SNP scoring with GAMMArrays: genomic analysis using multiplexed microsphere arrays
Author(s): Lance D. Green; Hong Cai; David C. Torney; Diane J. Wood; Francisco J. Uribe-Romeo; Lars Kaderali; John P. Nolan; P. Scott White
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Paper Abstract

We have developed a SNP scoring platform, yielding high throughput, inexpensive assays. The basic platform uses fluorescently labeled DNA fragments bound to microspheres, which are analyzed using flow cytometry. SNP scoring is performed using minisequencing primers and fluorescently labeled dideoxynucleotides. Furthermore, multiplexed microspheres make it possible to score hundreds of SNPs simultaneously. Multiplexing, coupled with high throughput rates allow inexpensive scoring of several million SNPs/day. GAMMArrays use universal tags that consist of computer designed, unique DNA tails. These are incorporated into each primer, and the reverse-component is attached to a discrete population of microspheres in a multiplexed set. This enables simultaneous minisequencing of many SNPs in solution, followed by capture onto the appropriate microsphere for multiplexed analysis by flow cytometry. We present results from multiplexed SNP analyses of bacterial pathogens, and human mtDNA variation. Analytes are performed on PCR amplicons, each containing numerous SNPs scored simultaneously. In addition, these assays easily integrate into conventional liquid handling automation, and require no unique instrumentation for setup and analysis. Very high signal-to-noise ratios, ease of setup, flexibility in format and scale, and low cost make these assays extremely versatile and valuable tools for a wide variety of SNP scoring applications.

Paper Details

Date Published: 21 June 2002
PDF: 8 pages
Proc. SPIE 4626, Biomedical Nanotechnology Architectures and Applications, (21 June 2002); doi: 10.1117/12.472096
Show Author Affiliations
Lance D. Green, Los Alamos National Lab. (United States)
Hong Cai, Los Alamos National Lab. (United States)
David C. Torney, Los Alamos National Lab. (United States)
Diane J. Wood, Los Alamos National Lab. (United States)
Francisco J. Uribe-Romeo, Los Alamos National Lab. (United States)
Lars Kaderali, Univ. of Cologne (United States)
John P. Nolan, Los Alamos National Lab. (United States)
P. Scott White, Los Alamos National Lab. (United States)

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

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