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.
Zineh
Issam
I
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
Welder
Gregory J
GJ
Langaee
Taimour Y
TY
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