Template-directed dye-terminator incorporation with fluorescence polarization detection for analysis of single nucleotide polymorphism implicated in sepsis

Bradley D. Freeman, Timothy G. Buchman, Sean McGarth, Arash Rafii Tabrizi, Barbara A. Zehnbauer

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Sepsis continues to be a common source of morbidity and mortality in critically ill patients. Single nucleotide polymorphisms (SNPs) present in genes encoding inflammatory mediators have been associated with predisposition and outcome in this syndrome. The use of high throughput SNP analysis in large epidemiological studies is necessary to more fully understand the genetic underpinnings of this disease. We adapted template-directed dye-terminator incorporation with fluorescence polarization detection (TDI-FP) to the analysis of eight SNPs implicated in mediating the sepsis syndrome: TNF-α (-308), INF-α (-238), TNF-β (+250), IL-1β (+3953), IL-6 (-174), IL-10 (-592), plasminogen activator inhibitor-1 (PAI-1 (-675)), and TLR4 299 (+1032). Optimization of PCR, amplicon purification, and template-directed dye-terminator incorporation reactions were necessary to achieve acceptable performance characteristics for these assays. Sequence validated samples served as controls. Using this method we were able to assign genotype in 99.3% of assays and identified 64 unique genotypes in samples obtained from 90 individuals. TDI-FP is a flexible and robust method of SNP detection that can be optimized in a systematic fashion. This method has potential advantages compared with other high throughput genotyping techniques and appears well suited to clinical situations requiring analysis of large numbers of samples.

Original languageEnglish
Pages (from-to)209-215
Number of pages7
JournalJournal of Molecular Diagnostics
Volume4
Issue number4
Publication statusPublished - Nov 2002
Externally publishedYes

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Fluorescence Polarization
Single Nucleotide Polymorphism
Sepsis
Coloring Agents
Plasminogen Activator Inhibitor 1
Genotyping Techniques
Genotype
Systemic Inflammatory Response Syndrome
Inborn Genetic Diseases
Interleukin-1
Critical Illness
Interleukin-10
Epidemiologic Studies
Interleukin-6
Morbidity
Polymerase Chain Reaction
Mortality
Genes

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Template-directed dye-terminator incorporation with fluorescence polarization detection for analysis of single nucleotide polymorphism implicated in sepsis. / Freeman, Bradley D.; Buchman, Timothy G.; McGarth, Sean; Tabrizi, Arash Rafii; Zehnbauer, Barbara A.

In: Journal of Molecular Diagnostics, Vol. 4, No. 4, 11.2002, p. 209-215.

Research output: Contribution to journalArticle

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