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Proceedings Paper

Rapid single nucleotide polymorphism detection for personalized medicine applications using planar waveguide fluorescence sensors
Author(s): James N. Herron; Samuel E. Tolley; Richard Smith; Douglas A. Christensen
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Paper 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.

Paper Details

Date Published: 25 February 2006
PDF: 10 pages
Proc. SPIE 6080, Advanced Biomedical and Clinical Diagnostic Systems IV, 60800Z (25 February 2006);
Show Author Affiliations
James N. Herron, Univ. of Utah (United States)
Samuel E. Tolley, Univ. of Utah (United States)
Richard Smith, Univ. of Utah (United States)
Douglas A. Christensen, Univ. of Utah (United States)

Published in SPIE Proceedings Vol. 6080:
Advanced Biomedical and Clinical Diagnostic Systems IV
Gerald E. Cohn; Warren S. Grundfest M.D.; David A. Benaron M.D.; Tuan Vo-Dinh, Editor(s)

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