At the high-throughput end of multiplex SNP genotyping, Illumina of San Diego, California, is currently beta testing the Sentrix Human-1 BeadChip, containing more than 100,000 SNPs, nearly 30,000 of which are located in genes, with another 40,000 within 10 kb of genes. The company is developing BeadChips containing 250,000 and 500,000 SNPs for release next year, which will make it possible to genotype 1 million SNPs on just a pair of chips.

Roche's LightTyper speeds up high-throughput genotyping. Credit: TOM MERCE/CLEVELAND CLINIC

Using a different approach to SNP genotyping, the LightTyper Genotyping System from Roche Applied Science of Indianapolis, Indiana, is designed for the heavy-duty end of the market, where thousands of samples may have to be genotyped each day. After PCR amplification of genomic samples in 96- or 384-well plates using a standard thermal cycler, plates are transferred directly to the LightTyper and genotyped within 10 minutes, using the melting points of fluorescently labelled probes hybridized with the SNPs as the detection system. Probe-target complexes with different melting points reflect the presence of different alleles, and show up as allele-specific peaks in the melting curves. Because many samples can be tested simultaneously, “the LightTyper instrument is mainly used for SNP genotyping, in particular for disease association studies,” says Burkhard Ziebolz of science communications at Roche Diagnostics in Mannheim, Germany.

The Luminex xMAP platform for multiplex genotyping is used by several genetic diagnostics service companies, including TmBioscience of Toronto, Ontario, which has developed the first Food and Drug Administration-approved multiplexed test for cystic fibrosis mutations, and Tepnel LifeCodes of Manchester, UK, whose speciality is HLA DNA typing.

For less-intensive SNP detection, the READIT SNP genotyping system from Promega of Madison, Wisconsin, can be scaled up or down. It uses the company's READase-mediated destabilization of perfectly matched probe-target complexes coupled with a luciferase reporter assay for the ATP generated. With appropriately designed probes, the system can detect SNPs, insertions, deletions and chromosomal translocation, and can estimate allele frequency and carry out allele-correlation studies. And PerkinElmer of Boston, Massachusetts, have SNP detection kits in their established AcycloPrime range.

Caitlin Smith