Multiplexed SNP genotyping using nanobarcode particle technology

Single-nucleotide polymorphisms (SNP) are the most common form of sequence variation in the human genome. Large-scale studies demand high-throughput SNP genotyping platforms. Here we demonstrate the potential of encoded nanowires for use in a particles-based universal array for high-throughput SNP g...

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Bibliographic Details
Published in:Analytical and bioanalytical chemistry Vol. 384; no. 3; pp. 658 - 666
Main Authors: Sha, Michael Y, Walton, Ian D, Norton, Scott M, Taylor, Micah, Yamanaka, Mark, Natan, Michael J, Xu, Chongjun, Drmanac, Snezana, Huang, Steve, Borcherding, Adam, Drmanac, Radoje, Penn, Sharron G
Format: Journal Article
Language:English
Published: Germany Berlin/Heidelberg : Springer-Verlag 01.02.2006
Subjects:
alleles
analysis
chemistry
cytochrome P-450
DNA
DNA - analysis
DNA - genetics
Encoded particles
genetics
Genotype
genotyping
gold
Humans
methods
nanoparticles
Nanoparticles - chemistry
nanorods
Nanotechnology
Nanotechnology - methods
Nanotubes
Nanotubes - chemistry
nanowires
oligonucleotides
polymerase chain reaction
Polymerase Chain Reaction - methods
Polymorphism, Single Nucleotide
Polymorphism, Single Nucleotide - genetics
Sensitivity and Specificity
silver
single nucleotide polymorphism
SNP genotyping
ISSN:1618-2642, 1618-2650
Online Access:Get full text
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Summary:Single-nucleotide polymorphisms (SNP) are the most common form of sequence variation in the human genome. Large-scale studies demand high-throughput SNP genotyping platforms. Here we demonstrate the potential of encoded nanowires for use in a particles-based universal array for high-throughput SNP genotyping. The particles are encoded sub-micron metallic nanorods manufactured by electroplating inert metals such as gold and silver into templates and releasing the resulting striped nanoparticles. The power of this technology is that the particles are intrinsically encoded by virtue of the different reflectivity of adjacent metal stripes, enabling the generation of many thousands of unique encoded substrates. Using SNP found within the cytochrome P450 gene family, and a universal short oligonucleotide ligation strategy, we have demonstrated the simultaneous genotyping of 15 SNP; a format requiring discrimination of 30 encoded nanowires (one per allele). To demonstrate applicability to real-world applications, 160 genotypes were determined from multiplex PCR products from 20 genomic DNA samples.
Bibliography:http://dx.doi.org/10.1007/s00216-005-0225-0
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ISSN:1618-2642
1618-2650
DOI:10.1007/s00216-005-0225-0