CSNP discovery by two-dimensional gene scanning (TDGS)

Challenges in the post-genomic era are to use genetic information in correlating individual gene variations (SNPs; single nucleotide polymorphisms, the most common form of genetic variation) with medically important parameters, such as disease susceptibility, individual responses to drugs and prognostic variables. What is missing is a high-throughput technology to identify all possible SNPs in essentially all human genes in population-based studies with high accuracy and speed in a cost-effective manner. Most tests advocated for their high throughput at low cost are actually SNP screening tests. That is, they screen samples for the presence of one or multiple previously identified SNPs. Such screening methods are only useful when all relevant SNPs in the genes of interest are known, which is presently not the case. Moreover, the usefulness of any one SNP varies enormously from population to population. Indeed, for the Korean population, where no information on possible sequence variation is available, a mutational scanning method, capable to detect all possible gene variations will be most useful. Two-Dimensional Gene Scanning (TDGS) is a high-throughput platform that enables to detect all possible SNPs in an entire gene in one gel under one set of conditions, with high sensitivity and specificity. TDGS is based on automated two-dimensional (2-D) DNA electrophoresis according to size and base pair sequence to detect DNA fragments containing all possible variations. Because the 2-D format permits the analysis of as many as 40 fragments of 250 bp on average in parallel, TDGS allows extensive multiplex PCR (megaplex PCR), i.e. up to 26 fragments in one single reaction, resulting in a significant cost reduction. TDGS tests are designed using a computer program to optimally position PCR primers around the relevant target sequences (exons). A simple automated 2-D instrument allows scanning all exons of a large gene in 8 different samples well within 3 hours. Using three different fluorophores this provides a throughput.