February 6, 2006
Nanobarcode Particles Determine Multiple Genotypes Simultaneously
With efforts underway to create an atlas of human cancer mutations, there will come a day when physicians will need to screen patients for dozens of possible gene mutations in order to characterize a given tumor type. Researchers at Nanoplex Technologies Inc., in Mountain View, CA, aim to provide an automated platform capable of providing just that type of screening capability using metallic nanorods with built-in barcodes.
Sharron Penn, Ph.D., and her colleagues have developed a method for depositing atoms of gold, platinum, and silver on templates so that the resulting nanorods have distinct striped patterns of the three metals. At the nanoscale, these stripes resemble the patterns of thick and thin lines that form the familiar barcodes found on millions of consumer items. And just as a laser-based optical reader can detect and analyze the different patterns of lines on a product’s barcode, each distinct pattern of gold, platinum, and silver lines can be identified based on the different reflectivity of adjacent metal stripes.
By forming just nine stripes of the three metals, Nanoplex investigators can create nearly 20,000 different barcodes. Proprietary software enables the identification of each distinct barcode using a conventional optical microscope.
In work reported in the journal Analytical and Bioanalytical Chemistry, Penn and her colleagues used their nanobarcode particles to analyze single nucleotide polymorphisms (SNPs), single base changes found throughout the human genome, in genes that code for proteins in the cytochrome P450 family. These proteins are involved in drug metabolism, and certain members of this family have been associated with cancer risk. Because the genes encoding this large family of proteins differ little among themselves, distinguishing among them in a rapid and reproducible manner has long been considered a technical challenge.
To distinguish among these many genes, the researchers created 30 probes using short sequences of single-stranded DNA linked to a series of nanobarcode particles. These nucleic acid sequences complement the known variable portions of the P450 gene family, that is, the gene sequences that code for specific P450 proteins. These sequences are known thanks to extensive studies of the P450 family.
A test with samples of human DNA showed that this system was capable of identifying each of the genetic variations that the test was designed to find. The investigators note, however, that the sensitivity of their system is not yet sufficient to enable real-time testing of typical human samples using existing methods of preparing DNA samples. The researchers are now working to improve the assay’s sensitivity.
This work is detailed in a paper titled, “Multiplexed SNP genotyping using nanobarcode particle technology.” Researchers from Callida Genomics, Inc., in Sunnyvale, CA, also participated in this study. This paper was published online in advance of print publication. An abstract is available through PubMed.