Development and cross-validation of sequencing-based assays for genotyping common polymorphisms of the CXCL5 gene.
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.
University of Florida College of Pharmacy, Department of Pharmacy Practice and Center for Pharmacogenomics, P.O. Box 100486, Gainesville, FL 32610, USA. zineh@cop.ufl.edu
Issam
I
Zineh
Gregory J
GJ
Welder
Taimour Y
TY
Langaee
D000483:Alleles; D001483:Base Sequence; D054365:Chemokine CXCL5; D019743:Chemokines, CXC / Q000235:genetics*; D005838:Genotype; D006801:Humans; D011110:Polymorphism, Genetic / Q000235:genetics*; D015203:Reproducibility of Results
C486263:CXCL5 protein, human; D054365:Chemokine CXCL5; D019743:Chemokines, CXC