Rapid single nucleotide polymorphism detection for personalized medicine applications using planar waveguide fluorescence sensors

James N. Herron; Samuel E. Tolley; Richard Smith; Douglas A. Christensen

doi:10.1117/12.669228

25 February 2006 Rapid single nucleotide polymorphism detection for personalized medicine applications using planar waveguide fluorescence sensors

James N. Herron, Samuel E. Tolley, Richard Smith, Douglas A. Christensen

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Proceedings Volume 6080, Advanced Biomedical and Clinical Diagnostic Systems IV; 60800Z (2006) https://doi.org/10.1117/12.669228
Event: SPIE BiOS, 2006, San Jose, California, United States

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, Samuel E. Tolley, Richard Smith, and 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); https://doi.org/10.1117/12.669228

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KEYWORDS

Planar waveguides

Sensors

Biosensors

Medicine

Waveguides

Diagnostics

Polymers

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