25 February 2006 Rapid single nucleotide polymorphism detection for personalized medicine applications using planar waveguide fluorescence sensors
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Abstract
Personalized medicine is an emerging field in which clinical diagnostics information about a patient's genotype or phenotype is used to optimize his/her pharmacotherapy. This article evaluates whether planar waveguide fluorescent sensors are suitable for determining such information from patient testing in point-of-care (POC) settings. The model system was Long QT Syndrome, a congenital disease associated with single nucleotide polymorphisms (SNPs) in genes encoding for cardiac ion channels. Three different SNP assay formats were examined: DNA/DNA hybridization, DNA/PNA hybridization (PNA: "peptide nucleic acid"), and single base extension (SBEX). Although DNA/DNA hybridization produced a strong intensity-time response for both wildtype and SNP analytes in a 5-min assay at 32°C, their hybridization rates differed by only 32.7%, which was insufficient for clinical decision-making. Much better differentiation of the two rates was observed at 53°C, where the wildtype's hybridization rate was two-thirds of its maximum value, while that of the SNP was essentially zero. Such all-or-nothing resolution would be adequate for clinical decision-making; however, the elevated temperature and precise temperature control would be hard to achieve in a POC setting. Results from DNA/PNA hybridization studies were more promising. Nearly 20-fold discrimination between wildtype and SNP hybridization rates was observed in a 5-min assay at 30°C, although the low ionic strength conditions required necessitated a de-salting step between sample preparation and SNP detection. SBEX was the most promising of the three, determining the absolute identity of the suspected polymorphism in a 5-min assay at 40°C.
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James N. Herron, James N. Herron, Samuel E. Tolley, Samuel E. Tolley, Richard Smith, Richard Smith, Douglas A. Christensen, Douglas A. Christensen, } "Rapid single nucleotide polymorphism detection for personalized medicine applications using planar waveguide fluorescence sensors", Proc. SPIE 6080, Advanced Biomedical and Clinical Diagnostic Systems IV, 60800Z (25 February 2006); doi: 10.1117/12.669228; https://doi.org/10.1117/12.669228
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