Multiplexed SNP genotyping using nanobarcode particle technology

Michael Y. Sha; Ian D. Walton; Scott M. Norton; Micah Taylor; Mark Yamanaka; Michael J. Natan; Chongjun Xu; Snezana Drmanac; Steve Huang; Adam Borcherding; Radoje Drmanac; Sharron G. Penn

doi:10.1007/s00216-005-0225-0

Multiplexed SNP genotyping using nanobarcode particle technology

Michael Y. Sha
, Ian D. Walton
, Scott M. Norton
, Micah Taylor
, Mark Yamanaka
, Michael J. Natan
, Chongjun Xu
, Snezana Drmanac
, Steve Huang
, Adam Borcherding
, Radoje Drmanac
, Sharron G. Penn

Nanoplex Technologies, Inc.
Callida Genomics Inc

Research output: Contribution to journal › Article › peer-review

60 Scopus citations

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.

Original language	English
Pages (from-to)	658-666
Number of pages	9
Journal	Analytical and Bioanalytical Chemistry
Volume	384
Issue number	3
DOIs	https://doi.org/10.1007/s00216-005-0225-0
State	Published - Feb 2006
Externally published	Yes

Bibliographical note

Funding Information:
Acknowledgements We would like to thank Glenn Davis for developing the NBSee Software and SNP database software for nanowire decoding and SNP data analysis, Griff Freeman, Frances Wong, Barry Simkins, and Gabriela Chakarova for expertise in nanowire synthesis, and Jay Shafto for help in robotic probe handling and probe validation. This work was funded by the National Institute of Standards and Technology (Grant 70NANB1H3028).

Funding

Acknowledgements We would like to thank Glenn Davis for developing the NBSee Software and SNP database software for nanowire decoding and SNP data analysis, Griff Freeman, Frances Wong, Barry Simkins, and Gabriela Chakarova for expertise in nanowire synthesis, and Jay Shafto for help in robotic probe handling and probe validation. This work was funded by the National Institute of Standards and Technology (Grant 70NANB1H3028).

Funders	Funder number
National Institute of Standards and Technology	70NANB1H3028

Keywords

Cytochrome P450
Encoded particles
Nanotechnology
Nanowires
SNP genotyping

Access to Document

10.1007/s00216-005-0225-0

Cite this

@article{119ad4ed609b42e0b2b79019d7969430,

title = "Multiplexed SNP genotyping using nanobarcode particle technology",

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.",

keywords = "Cytochrome P450, Encoded particles, Nanotechnology, Nanowires, SNP genotyping",

author = "Sha, \{Michael Y.\} and Walton, \{Ian D.\} and Norton, \{Scott M.\} and Micah Taylor and Mark Yamanaka and Natan, \{Michael J.\} and Chongjun Xu and Snezana Drmanac and Steve Huang and Adam Borcherding and Radoje Drmanac and Penn, \{Sharron G.\}",

note = "Funding Information: Acknowledgements We would like to thank Glenn Davis for developing the NBSee Software and SNP database software for nanowire decoding and SNP data analysis, Griff Freeman, Frances Wong, Barry Simkins, and Gabriela Chakarova for expertise in nanowire synthesis, and Jay Shafto for help in robotic probe handling and probe validation. This work was funded by the National Institute of Standards and Technology (Grant 70NANB1H3028).",

year = "2006",

month = feb,

doi = "10.1007/s00216-005-0225-0",

language = "אנגלית",

volume = "384",

pages = "658--666",

journal = "Analytical and Bioanalytical Chemistry",

issn = "1618-2642",

publisher = "Springer Science and Business Media Deutschland GmbH",

number = "3",

}

TY - JOUR

T1 - Multiplexed SNP genotyping using nanobarcode particle technology

AU - Sha, Michael Y.

AU - Walton, Ian D.

AU - Norton, Scott M.

AU - Taylor, Micah

AU - Yamanaka, Mark

AU - Natan, Michael J.

AU - Xu, Chongjun

AU - Drmanac, Snezana

AU - Huang, Steve

AU - Borcherding, Adam

AU - Drmanac, Radoje

AU - Penn, Sharron G.

N1 - Funding Information: Acknowledgements We would like to thank Glenn Davis for developing the NBSee Software and SNP database software for nanowire decoding and SNP data analysis, Griff Freeman, Frances Wong, Barry Simkins, and Gabriela Chakarova for expertise in nanowire synthesis, and Jay Shafto for help in robotic probe handling and probe validation. This work was funded by the National Institute of Standards and Technology (Grant 70NANB1H3028).

PY - 2006/2

Y1 - 2006/2

N2 - 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.

AB - 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.

KW - Cytochrome P450

KW - Encoded particles

KW - Nanotechnology

KW - Nanowires

KW - SNP genotyping

UR - https://www.scopus.com/pages/publications/32544444286

U2 - 10.1007/s00216-005-0225-0

DO - 10.1007/s00216-005-0225-0

M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???

C2 - 16421712

AN - SCOPUS:32544444286

SN - 1618-2642

VL - 384

SP - 658

EP - 666

JO - Analytical and Bioanalytical Chemistry

JF - Analytical and Bioanalytical Chemistry

IS - 3

ER -

Multiplexed SNP genotyping using nanobarcode particle technology

Abstract

Bibliographical note

Funding

Keywords

Access to Document

Other files and links

Fingerprint

Cite this