Single nucleotide polymorphism (SNP) analysis systems work on the premise that tiny aberrations can snowball into giant effects. Rooting out a single errant nucleotide provides valuable information in dealing with serious diseases. The latest SNPs are entering the market with great acclaim from researchers, who welcome the capability to generate faster and better results.
These researchers have a very good reason for desiring more efficient means of analyzing SNPs; estimates reveal that up to 30 million SNPs exist in the human genome. So far, “many of the 7 million variants that exist with frequencies above 5% in the human population have been identified,” according to a short paper published in a 2005 issue of Nature Genetics (37:1299-1300); and much work lies ahead, since “current genotyping technologies are limited to testing 100,000–500,000 variants in a collection of individuals in any given association study.”
About one out of every 300 base pairs is a SNP; most of these lie outside coding regions. The differences lead to humans’ amazing diversity in skin and hair color, height, creativity, and intelligence. At the same time, SNPs also cause one person to be more susceptible to developing certain diseases, or to be more responsive to certain medical therapies than others. Some SNPs can lead to near-certain suffering, in cases of sickle cell anemia and cystic fibrosis, for example.
Nucleic acid microarrays were once the leading high-throughput method for studying SNPs. While microarray pioneer Affymetrix now provides options specifically to expedite SNP analysis, other companies have stepped up to offer alternate strategies. Bead-based assays have become increasingly popular. Like microarrays, beads display hundreds or thousands of oligonucleotides that could potentially bind to the sample. You can simultaneously screen more than one sample by using fluorescent probes of different colors. In addition to their multiplexing capabilities, bead assays can be performed without the hefty expense of automated equipment. Flow cytometers, usually standard equipment, can serve the purpose of reading and analyzing assay results.
But if you do have the money and need more speed, consider investing in an automated system that takes on all of the manual work and frees your time to analyze and interpret the results. In addition to those that handle bead assays, you can choose systems that that automatically perform capillary electrophoresis. These systems minimize the errors and variability introduced by human intervention, preventing the need for costly and time-consuming repetition. Many automated systems come with the option to add an integrated plate stacker, internal bar code reader, reagent-dispensing liquid handler, and other useful accessories.
More speed doesn’t necessarily mean more money. Don’t forget to avail yourself of the many free databases that could steer you in the right direction. In return, you can deposit your own results for others to share. To get started, take a look at the SNP-analyzing items below.