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The Tebbutt Laboratory is working in the field of human genetic variation and the relationships of single nucleotide polymorphisms (SNPs) with complex inherited diseases such as asthma, chronic obstructive pulmonary disease (COPD), and the systemic inflammatory response syndrome (SIRS). Inflammation and innate immunity responses are pathways common to many complex diseases of the cardiovascular and pulmonary systems, and there is much interest in elucidating gene-gene and gene-environment interactions that might contribute to differences in disease susceptibility and outcomes between individuals. An ability to rapidly and economically determine multiple SNP genotypes/haplotypes in any individual patient, across multiple genes involved in pathophysiological pathways relevant to inflammatory disease, is essential for such research and may become highly relevant in future clinical applications (e.g., pharmacogenomics and personalized medicine). Microarray-based genotyping methodologies such as arrayed primer extension (APEX) offer the greatest potential for economic, sample-specific application due to their ability to simultaneously and rapidly (assay chemistry takes 20 minutes) interrogate multiple genetic markers (SNPs) in an individual. A strong focus of the group is to further develop and utilize APEX as a low-cost, accurate, and robust genotyping tool for research, clinical, and industrial applications.
www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml
www.snpchart.ca
The chemistry, enzymology, and analysis systems for microarray-based genotyping by minisequencing (e.g., APEX) have much scope for further improvement. In addition, solely as a research platform, APEX represents an important open-source assay device with which to develop and validate novel chemistries, enzymologies, and image analysis and statistical algorithms, representing fundamental basic research in these disciplines. To our knowledge, the research described here is the first report of four-color direct single-base minisequencing on micro-arrays using fluorescently labeled deoxynucleotides instead of dideoxynucleotides. Considerable cost-savings are associated with using fluorescent dNTPs, rather than fluorescent ddNTPs, and there is a wider selection of fluoro-phores available with dNTPs, as well as more of a selection of DNA polymerase enzymes. Further studies might investigate the biochemical mechanisms causing the effective chain termination (possibly involving steric hindrance through the fluorophores), adding to our knowledge of nucleic acids and DNA enzymes, and perhaps leading to the development of new and improved minisequencing reagents.
Deoxynucleotides can replace dideoxynucleotides in minisequencing by arrayed primer extension, p. 331.
