Scientists at the ARUP Institute for Clinical and Experimental Pathology (www.aruplab.com) have developed a technology utilizing hybridization probes to identify SNP haplotypes in one step. "Current techniques for haplotyping are very complicated," explains Genevieve Pont-Kingon, Ph.D., senior research scientist.
Dr. Pont-Kingdon said her group was able to design a hybridization probe to cover two SNPs that are within a 100 nucletotide range. "We found if you make a deletion inside the probe compared to the template, the template sequence loops out, and then the probe binds continuously on the template."
She adds that each combination of SNP has a specific melting temperature (reflects probe stability due to length, nucleotide composition, and homology to template) that can be recorded by fluorescence.
As an example of how this technology works, the group used three haplotypes found in the beta 2-adrenergic receptor gene and characterized by three different SNP combinations. "We were able to discover two previously undescribed haplotypes in this gene using our probe technology," says Dr. Pont-Kingdon.
Potential applications for this new technology include pharmacogenomicsfor example, using the beta 2-adrenergic receptor gene to examine the genetic variation in this receptor as a response to beta-blockers. The technology can also directly determine haplotypes of multiple polymorphisms in a closed-tube environment, making it a potential clinical genetic test from individual samples.
Haplotype analysis with hybridization probes on high throughput instruments would enable analysis of large numbers of samples necessary for association studies and pharmacogenomic trials. "We expect that within the next few years we will be able to do haplotyping in the clinical lab," adds Dr. Pont-Kingdon.
ParAllele BioScience (www.parallelebio.com) presented information on identifying biomarkers for cancer therapeutics via analysis of germline and somatic mutations. The company's platform is based on two proprietary technologies: Molecular Inversion Probes (MIP) and Mismatch Repair Detection (MRD).
"We are able to work with SNPs that are most relevant to the researchers because we have a highly specific technology and can multiplex to very high levels: over 20,000-plex has been demonstrated," states Thomas Willis, Ph.D., CSO.
"By combining our technology with the whole-genome mapping products of Affymetrix, we will jointly be able to offer a broad set of genetics research products." The company recently announced a definitive agreement to be acquired by Affymetrix.
MIP enables copy number analysislooks for all types of chromosomal re-arrangements, including small deletions and amplifications, as well as mitotic recombinations, which change allele ratio, but not overall copy number. In addition, the technology enables highly quantitative expression analysis. MRD is used for somatic mutation detection, and according to the company, has advantages over sequencing.
"This technology allows hundreds of genes to be scanned for mutations in a single reaction. Conventional sequencing allows only the analysis of a single gene segment at a time," explains Dr. Willis.