Development and cross-validation of sequencing-based assays for genotyping common polymorphisms of the CXCL5 gene

Abstract

Background: Epithelial neutrophil activating peptide (ENA-78) is encoded by the polymorphic CXCL5 gene and is a recruiter and activator of neutrophils. Furthermore, ENA-78 may be involved in pathological inflammatory processes and variable drug responses. Methods: To facilitate future disease-gene and pharmacogenetic investigation of ENA-78, we developed and cross-validated medium- to high-throughput genotyping assays for 2 commonly occurring CXCL5 polymorphisms (rs352046 and rs425535). Furthermore, we compared allele and genotype frequencies in a U.S. population with those of a previously studied European population. Results: There was 100% genotype concordance between the 2 methods used (Pyrosequencing® and TaqMan®). Variant allele frequencies for rs352046 were consistent between the U.S. (16%) and European (16%) populations, while the rs425535 variant allele was more than twice as high in the European cohort (38% vs. 16%). There was complete linkage of genotypes at both loci in our population. Conclusions: The distribution of variant alleles for the 2 polymorphisms studied should be further evaluated in other populations. In addition, our data highlight the importance of assay validation using multiple platforms. © 2006 Elsevier B.V. All rights reserved.