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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Vydané v:	Analytical and bioanalytical chemistry Ročník 384; číslo 3; s. 658 - 666
Hlavní autori:	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
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	Germany Berlin/Heidelberg : Springer-Verlag 01.02.2006
Predmet:	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
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Abstract	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.
AbstractList	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. 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.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.
Author	Borcherding, Adam Xu, Chongjun Walton, Ian D Norton, Scott M Penn, Sharron G Drmanac, Radoje Drmanac, Snezana Sha, Michael Y Huang, Steve Taylor, Micah Yamanaka, Mark Natan, Michael J
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SubjectTerms	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
Title	Multiplexed SNP genotyping using nanobarcode particle technology
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