Multiplexed SNP genotyping using nanobarcode particle technology

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.
January 2006
Analytical & Bioanalytical Chemistry;Jan2006, Vol. 384 Issue 3, p658
Academic Journal
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.


Related Articles

  • A highly informative SNP linkage panel for human genetic studies. Murray, Sarah Shaw; Oliphant, Arnold; Shen, Richard; McBride, Celeste; Steeke, Rhoberta J; Shannon, Stuart G; Rubano, Todd; Kermani, Bahram G; Fan, Jian-Bing; Chee, Mark S; Hansen, Mark S T // Nature Methods;Nov2004, Vol. 1 Issue 2, p113 

    We have developed a highly informative set of single-nucleotide polymorphism (SNP) assays designed for linkage mapping of the human genome. These assays were developed on a robust multiplexed assay system to provide a combination of very high accuracy and data completeness with high throughput...

  • Singleton SNPs in the human genome and implications for genome-wide association studies. Xiayi Ke; Taylor, Martin S.; Cardon, Lon R. // European Journal of Human Genetics;Apr2008, Vol. 16 Issue 4, p506 

    The human genome is estimated to contain one single nucleotide polymorphism (SNP) every 300 base pairs. The presence of LD between SNP markers can be used to save genotyping cost via appropriate SNP tagging strategies, whereas absence or low level of LD between markers generally increase...

  • Multiple testing in genome-wide association studies via hidden Markov models. Zhi Wei; Wenguang Sun; Kai Wang; Hakonarson, Hakon // Bioinformatics;Nov2009, Vol. 25 Issue 21, p2802 

    Motivation: Genome-wide association studies (GWAS) interrogate common genetic variation across the entire human genome in an unbiased manner and hold promise in identifying genetic variants with moderate or weak effect sizes. However, conventional testing procedures, which are mostly P-value...

  • Expanding Hapmap. Rusk, Nicole // Nature Methods;Oct2010, Vol. 7 Issue 10, p780 

    The article reports on the expansion of the human haplotype map (HapMap) project to include single-nucleotide polymorphisms (SNPs) of lower frequency that cannot be captured by the current generation of microarrays. It mentions the goal of the HapMap, a 1000 genomes project which was based on 11...

  • A structural map of the human genome. Kiermer, Veronique // Nature Methods;Jul2005, Vol. 2 Issue 7, p484 

    Pursuing a great promise of the human genome project, a plethora of studies is being carried out to find single-nucleotide polymorphisms (SNPs) associated with disease susceptibility. But these are not the only source of variation between individuals.

  • Race, Ethnicity, and Science: The Haplotype Genome Project. Murray, Thomas // Hastings Center Report;Sep/Oct2001, Vol. 31 Issue 5, p7 

    Presents information on the Haplotype Genome Project. Detection of single nucleotide polymorphisms; Focus of the project; Challenges posed by the issues of race and ethnicity.

  • Mapping complex traits with single nucleotide polymorphisms. Zhao, Lue Ping; Aragaki, Corinne; Hsu, Li; Quiaoit, Filemon // Nature Genetics;Nov99 Supplement, Vol. 23, p84 

    Presents an abstract for the article on mapping complex human genes with single nucleotide polymorphisms.

  • Whole-genome genotyping with the single-base extension assay. Steemers, Frank J.; Weihua Chang; Lee, Grace; Barker, David L.; Shen, Richard; Gunderson, Kevin L. // Nature Methods;Jan2006, Vol. 3 Issue 1, p31 

    We describe an efficient, accurate and robust whole-genome genotyping (WGG) assay based on a two-color, single-base extension (SBE), single-nucleotide polymorphism (SNP)-scoring step. We report genotyping results for biallelic International HapMap quality control (QC) SNPs using a single probe...

  • Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms. Cheng, Tammy M. K.; Yu-En Lu; Vendruscolo, Michele; Lio', Pietro; Blundell, Tom L. // PLoS Computational Biology;Jul2008, Vol. 4 Issue 7, p1 

    Recent analyses of human genome sequences have given rise to impressive advances in identifying non-synonymous single nucleotide polymorphisms (nsSNPs). By contrast, the annotation of nsSNPs and their links to diseases are progressing at a much slower pace. Many of the current approaches to...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics