title: Simultaneous genotyping of rs12979860 and rs8099917 variants near the IL28B locus associated with HCV clearance and treatment response.
abstract: Recent genome-wide association studies have identified two host single-nucleotide polymorphisms (SNPs) near the IL28B gene (rs12979860 C/T and rs8099917 T/G) that are associated with sustained virological response in patients infected with the hepatitis C virus. Herein, we describe a rapid multiplexed dual-color fluorescence resonance energy transfer (FRET) probe assay that accurately genotypes for both SNPs simultaneously. A single-nucleotide extension assay was also developed for verification of genotypes. Agreement (100%) was observed in genotype calls between the FRET and single-nucleotide extension methods for both SNPs, yielding 100% analytical sensitivity and specificity. By using the FRET assay, 443 samples of varying ethnic backgrounds were genotyped and six different compound genotypes (rs12979860/rs8099917) were detected in whites, Asians, Middle Easterners, Hispanics, and African Americans, at the following frequencies: CC/TT (39.2%, 78.9%, 40.0%, 33.9%, and 16.8%), CT/TT (20.8%, 0%, 40%, 9.3%, and 37.0%), TT/TT (2.4%, 0%, 0%, 3.4%, and 35.3%), CT/TG (24.0%, 19.7%, 20%, 39.8%, and 3.4%), TT/TG (8.0%, 1.4%, 0%, 3.4%, and 5.9%), and TT/GG (5.6%, 0%, 0%, 10.2%, and 1.7%), respectively. The multiplexed FRET assay can be used to effectively genotype for both SNPs in a single tube, with high analytical sensitivity and specificity.
authors.affiliation: Associated Regional and University Pathologists (ARUP) Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108-1221, USA. roberta.melis@aruplab.com
authors.forename: Roberta
authors.initials: R
authors.lastname: Melis
authors.forename: Christiane
authors.initials: C
authors.lastname: Fauron
authors.forename: Gwendolyn
authors.initials: G
authors.lastname: McMillin
authors.forename: Elaine
authors.initials: E
authors.lastname: Lyon
authors.forename: Brian
authors.initials: B
authors.lastname: Shirts
authors.forename: Lindsey M
authors.initials: LM
authors.lastname: Hubley
authors.forename: Patricia R
authors.initials: PR
authors.lastname: Slev
mesh_terms: D031541:Fluorescence Resonance Energy Transfer / Q000379:methods; D005787:Gene Frequency; D056726:Genetic Association Studies; D056426:Genetic Loci; D006239:Haplotypes; D016174:Hepacivirus; D019698:Hepatitis C, Chronic / Q000235:genetics*; D006801:Humans; D007372:Interferons; D007378:Interleukins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D044366:Transition Temperature; D016896:Treatment Outcome; D000095022:Interferon Lambda
chemical_list: D007372:Interferons; D007378:Interleukins; C000624353:interferon-lambda, human; D000095022:Interferon Lambda