“Spot-On” SNP Genotyping
- Exelixis, Inc., South San Francisco, California 94083–0511 USA
This extract was created in the absence of an abstract.
As we enter the post-genomic era, where complete reference genome sequences are a given, analyzing the variation among individual genomes is an area of intense investigation. One of the most common forms of genomic variation is single nucleotide polymorphisms, or SNPs. The “science of SNPs” has become a heavy industry, as evidenced by the proliferation of methods for genotyping and deployment of entire commercial enterprises devoted to research centered on SNPs. Why are we seeing such keen interest in these technologies?
Applications that utilize SNPs are cropping up in diverse areas of research. Undoubtedly, the area where SNPs are receiving the most attention is their use as genetic markers for the study of complex human traits and pharmacogenomics. Genome-wide complements of SNPs are now being developed as genetic tools in model organisms such asArabidopsis, Drosophila, and C. elegans. SNPs are finding favor as markers for genetic crosses and selective breeding strategies in livestock and plants of agricultural importance. All of these applications demand a technology that provides simple, robust, highly accurate and cost-effective genotyping of large numbers of SNPs on hundreds or thousands of individuals. Unlike DNA sequencing, where separation-based dideoxy sequencing predominates, no single technology for scoring SNPs has become a widely accepted standard. In this issue, Pastinen and colleagues present a novel array-based method for SNP genotyping (Pastinen et al. 2000).
Array of Light
The genotyping system developed by groups at the National Public Health Institute of Finland and Uppsala University uses allele-specific oligonucleotides on microarrays as templates for primer extension-based genotyping (Figure 1A). The technique, derived from earlier work of the same group (Pastinen et al. 1997), has several features that facilitate high-throughput genotyping. In order to extract the genomic sequence harboring the SNP, Pastinen and colleagues developed a two-step process whereby the sequence is first …
