title: Multiplexed SNP genotyping using the Qbead system: a quantum dot-encoded microsphere-based assay.
abstract: We have developed a new method using the Qbead system for high-throughput genotyping of single nucleotide polymorphisms (SNPs). The Qbead system employs fluorescent Qdot 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.
authors.affiliation: Quantum Dot Corporation, 26118 Research Road, Hayward, CA 94545, USA.
authors.forename: Hongxia
authors.initials: H
authors.lastname: Xu
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Sha
authors.forename: Edith Y
authors.initials: EY
authors.lastname: Wong
authors.forename: Janet
authors.initials: J
authors.lastname: Uphoff
authors.forename: Yanzhang
authors.initials: Y
authors.lastname: Xu
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Treadway
authors.forename: Anh
authors.initials: A
authors.lastname: Truong
authors.forename: Eamonn
authors.initials: E
authors.lastname: O'Brien
authors.forename: Steven
authors.initials: S
authors.lastname: Asquith
authors.forename: Michael
authors.initials: M
authors.lastname: Stubbins
authors.forename: Nigel K
authors.initials: NK
authors.lastname: Spurr
authors.forename: Eric H
authors.initials: EH
authors.lastname: Lai
authors.forename: Walt
authors.initials: W
authors.lastname: Mahoney
mesh_terms: D004247:DNA / Q000737:chemistry / Q000235:genetics; D004252:DNA Mutational Analysis / Q000295:instrumentation / Q000379:methods*; D005260:Female; D005838:Genotype; D006801:Humans; D008297:Male; D008863:Microspheres; D016133:Polymerase Chain Reaction / Q000295:instrumentation / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012680:Sensitivity and Specificity
chemical_list: D004247:DNA