SNP detection and scoring methods are many and various. Two recurrent themes are elegant simplicity and advanced technology. An effective method recently developed by the HGBASE team is Dynamic Allele-Specific Hybridization. Currently, most procedures involve target sequence PCR amplification, a burden that limits possibilities for scale-up and automation. This is equally true for the much acclaimed miniature hybridisation array (DNA-chip) concept.Genomic level scoring of cSNPs presents another largely unrecognized hurdle due to the possible existence (usually unknown)of processed pseudogenes.
These are the articles on the technology mentioned above (in PDF):
Dynamic Allele-Specific Hybridization (Articles).pdf
Dynamic Allele-Specific Hybridization (Method).pdf
For more, you may visit the SNP Consortium's protocol page ( http://snp.cshl.org/index.html.en ), there is a lot of detailed information on the detection technology.