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Nucleic Acids Research, 2003, Vol. 31, No. 8 e43
© 2003 Oxford University Press

Multiplexed SNP genotyping using the QbeadTM system: a quantum dot-encoded microsphere-based assay

Hongxia Xu, Michael Y. Sha, Edith Y. Wong, Janet Uphoff, Yanzhang Xu, Joseph A. Treadway, Anh Truong, Eamonn O’Brien1, Steven Asquith1, Michael Stubbins1, Nigel K. Spurr2, Eric H. Lai2 and Walt Mahoney

Quantum Dot Corporation, 26118 Research Road, Hayward, CA 94545, USA, 1 Discovery Genetics, GlaxoSmithKline R&D, New Frontiers Science Park, Third Avenue, Harlow, Essex CM19 5AW, UK and 2 Discovery Genetics, GlaxoSmithKline Inc., 5 Moore Drive, RTP, NC 27709, USA

*To whom correspondence should be addressed. Tel: +1 510 887 8775; Fax: +1 510 783 9729; Email: msha{at}qdots.com

We have developed a new method using the QbeadTM system for high-throughput genotyping of single nucleotide polymorphisms (SNPs). The Qbead system employs fluorescent QdotTM semiconductor nanocrystals, also known as quantum dots, to encode microspheres that subsequently can be used as a platform for multiplexed assays. By combining mixtures of quantum dots with distinct emission wavelengths and intensities, unique spectral ‘barcodes’ are created that enable the high levels of multiplexing required for complex genetic analyses. Here, we applied the Qbead system to SNP genotyping by encoding microspheres conjugated to allele-specific oligonucleotides. After hybridization of oligonucleotides to amplicons produced by multiplexed PCR of genomic DNA, individual microspheres are analyzed by flow cytometry and each SNP is distinguished by its unique spectral barcode. Using 10 model SNPs, we validated the Qbead system as an accurate and reliable technique for multiplexed SNP genotyping. By modifying the types of probes conjugated to microspheres, the Qbead system can easily be adapted to other assay chemistries for SNP genotyping as well as to other applications such as analysis of gene expression and protein–protein interactions. With its capability for high-throughput automation, the Qbead system has the potential to be a robust and cost-effective platform for a number of applications.


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