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Genotyping of single nucleotide polymorphisms in cytokine genes using real-time PCR allelic discrimination technology.

Authors
Johnson-VJ; Yucesoy-B; Luster-MI
Source
Cytokine 2004 Sep; 27(6):135-141
NIOSHTIC No.
20025454
Abstract
Single nucleotide polymorphisms (SNPs), particularly those within regulatory regions of genes that code for cytokines often impact expression levels and can be disease modifiers. Investigating associations between cytokine genotype and disease outcome provides valuable insight into disease etiology and potential therapeutic intervention. Traditionally, genotyping for cytokine SNPs has been conducted using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), a low throughput technique not amenable for use in large-scale cytokine SNP association studies. Recently, Taqman real-time PCR chemistry has been adapted for use in allelic discrimination assays. The present study validated the accuracy and utility of real-time PCR technology for a number of commonly studied cytokine polymorphisms known to influence chronic inflammatory diseases. We show that this technique is amenable to high-throughput genotyping and overcomes many of the problematic features associated with PCR-RFLP including post-PCR manipulation, non-standardized assay conditions, manual allelic identification and false allelic identification due to incomplete enzyme digestion. The real-time PCR assays are highly accurate with an error rate in the present study of <1% and concordance rate with PCR-RFLP genotyping of 99.4%. The public databases of cytokine polymorphisms and validated genotyping assays highlighted in the present study will greatly benefit this important field of research.
Keywords
Nucleotides; Genes; Etiology; Diseases; Chronic-inflammation; Chronic-degenerative-diseases
Contact
Toxicology and Molecular Biology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, 1095 Willowdale Road, Mail Stop 3014, Morgantown, WV 26505-2888, USA
CODEN
CYTIE9
Publication Date
20040921
Document Type
Journal Article
Email Address
vjohnson3@cdc.gov
Fiscal Year
2004
NTIS Accession No.
NTIS Price
Issue of Publication
6
ISSN
1043-4666
NIOSH Division
HELD
Priority Area
Disease and Injury: Asthma and Chronic Obstructive Pulmonary Disease
Source Name
Cytokine
State
WV
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