Tools for screening and validation

Taqman SNP Genotyping Assays, developed by Applied Biosystems, are a state-of-the-art technology for screening and validation of polymorphisms. Recently Applied Biosystems introduced two new products to complement this offering; the high throughput Taqman Open Array Genotyping System and Taqman Copy Number Assays.

NGP. What is genotyping, and what are its applications in disease prevention?
XC. Genotyping refers to the process of determining an individual’s genotype. SNPs are currently the most commonly studied genetic variation, although microsatellites and STRs have been widely used in the past and new markers, such as CNV (copy number variants), are of increasing interest to researchers. The ultimate goal of this analysis is to find links between a disease (or group of diseases) and its genetic background. Advances in the technologies available have allowed researchers to analyse thousands, or even millions, of SNPs to discover disease-associated genes, and validate results by replicating studies with larger cohorts of samples using technologies like Taqman SNP Genotyping Assays.

NGP. Why is genotyping important in clinical research?
XC. Clinical studies aim to discover panels of SNPs or other genetic markers that can be used in the prevention, prognosis or treatment decision of complex diseases. These biomarker panels often include polymorphisms of high clinical relevance, such as those located in DME (drug metabolising enzyme) genes. As they affect an individual’s drug responses, genes that code for the DMEs represent one of the most important classes of genetic variation in drug development studies. Analysis of SNPs in these genes is very important during the drug development phase, as this can indicate how a patient will metabolise the candidate drug. As a simple example, grouping patients into low, medium or high metabolisers can help researchers adjust dosage to improve drug efficiency. This strategy is called pharmacogenetics, and is important for the future of personalised medicine. Applied Biosystems’ DME Taqman SNP Genotyping Assays incorporate over 2,600 high value polymorphisms located in regulatory elements and coding regions of 220 drug metabolism and transporter genes. Later this year, users will be able to customise the Taqman Array Platform (microfluidic card) for DME genotyping research, allowing simultaneous analysis of eight samples for up to 96 SNPs.

NGP. What benefits does Applied Biosystems’ new high throughput genotyping system provide to life scientists? How does it differ from similar systems?
XC. The recently launched Taqman OpenArray Genotyping System combines Taqman SNP Genotyping Assays with the massively parallel OpenArray technology, allowing researchers to analyse more than 90,000 genotypes per day at low cost and with a simple laboratory set-up. The nanoliter sample volumes required for the Taqman technology permit a very simple workflow, with the excellent call rates critical to the success of this kind of research. Unlike other technologies, the Taqman OpenArray Genotyping System supports full analysis from DNA to results, with customers able to choose from more than 4.5 million pre-designed assays, or custom designed assays to suit any gene for any species. These assays are ready to run on OpenArray, with no hidden costs coming from oligo fees or third party consumables that may hamper the workflow. With this system Applied Biosystems delivers market-leading performance, support, training and services to ensure customer satisfaction for high throughput genotyping applications.

NGP. What do you believe will be the most important developments in genotyping over the next few years?
XC. Next generation sequencing is an exciting new technology being used by laboratories conducting disease-association studies. Re-sequencing of a large number of individuals will bring more genetic markers (SNPs and CNVs), so there will be increasing demand for simple yet effective technologies for validation and commercialisation of biomarker panels. To complement the SNP assays portfolio, Applied Biosystems has recently launched the Taqman Copy Number Assays. This solution is comprised of more than 1.6 million pre-designed assays, as well as a custom design pipeline, with specific analysis software to provide a platform for all researchers interested in CNV screening and validation of array CGH.

Xavier Cristina Ph.D. is the European Business Development Manager for the Molecular Biology Systems Division at Applied Biosystems, part of Life Technologies. After completing a Ph.D. in Microbiology and Biochemistry, Xavier joined Applied Biosystems in 2000 and has developed his career in various positions in the company.