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Nucleic Acids Research 2005 33(2):e15; doi:10.1093/nar/gni017
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Published online 19 January 2005

© 2005, the authors Nucleic Acids Research, Vol. 33 No. 2 © Oxford University Press 2005; all rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.

Methods Online

SNP identification in unamplified human genomic DNA with gold nanoparticle probes

Y. Paul Bao*, Martin Huber, Tai-Fen Wei, Sudhakar S. Marla, James J. Storhoff and Uwe R. Müller

Nanosphere Inc. 4088 Commercial Ave., Northbrook, IL 60062, USA

*To whom correspondence should be addressed. Tel: +1 847 400 9150; Fax: +1 847 400 9199; Email: pbao{at}nanosphere.us

Received November 19, 2004. Revised December 23, 2004. Accepted December 23, 2004.

Single nucleotide polymorphisms (SNPs) comprise the most abundant source of genetic variation in the human genome. SNPs may be linked to genetic predispositions, frank disorders or adverse drug responses, or they may serve as genetic markers in linkage disequilibrium analysis. Thus far, established SNP detection techniques have utilized enzymes to meet the sensitivity and specificity requirements needed to overcome the high complexity of the human genome. Herein, we present for the first time a microarray-based method that allows multiplex SNP genotyping in total human genomic DNA without the need for target amplification or complexity reduction. This direct SNP genotyping methodology requires no enzymes and relies on the high sensitivity of the gold nanoparticle probes. Specificity is derived from two sequential oligonucleotide hybridizations to the target by allele-specific surface-immobilized capture probes and gene-specific oligonucleotide-functionalized gold nanoparticle probes. Reproducible multiplex SNP detection is demonstrated with unamplified human genomic DNA samples representing all possible genotypes for three genes involved in thrombotic disorders. The assay format is simple, rapid and robust pointing to its suitability for multiplex SNP profiling at the ‘point of care’.

Correspondence may also be addressed to Uwe R. Müller. Tel: +1 847 400 9103; Fax: +1 847 400 9199; Email: umuller{at}nanosphere.us


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