Table 1.
Details of PCR amplicons used to examine SNP locations in IL28B and the corresponding reverse complement (RC) regions of IL28A.
Table 2.
TaqMan® amplification primers and detection probes for the rs12979860 genotyping assay.
Figure 1.
Schematic showing IL28 genes, SNP locations and areas of sequence homology.
Illustration of the relative locations of the IL28A and IL28B genes on the forward and reverse DNA strands on chromosome 19. The shaded boxes indicate regions of the inverted duplication with >95% sequence identity. The direction of the shaded gradient indicates the orientation of the match. SNP identifiers in blue were unique to the IL28B region, whereas SNPs highlighted in other colors were present in the IL28B region as well as a corresponding region in IL28A.
Figure 2.
Sequence alignments surrounding six of the treatment response associated SNPs.
Alignment comparing 50 bp sequence surrounding SNP locations in IL28B reference sequence from NCBI genome build 37 and the corresponding reverse complement regions of IL28A reference sequence (RC ref). SNP identifiers (color coded to match Figure 1) and their respective alleles are shown. Ancestral alleles were obtained from dbSNP, except for those indicated by +; in these cases, the allele was based upon alignment of gorilla, chimpanzee, macaque and orangutan sequences. SNP locations on each alignment are highlighted in red. The asterisk denotes sequence identity.
Table 3.
Allele frequencies of SNPs unique to IL28B region.
Table 4.
Allele frequencies of IL28B SNPs and corresponding regions of IL28A.
Figure 3.
Sequence alignment of IL28B and IL28A used to design the rs12979860 genotyping assay.
Clustal W alignment of a portion of the IL28B gene surrounding rs12979860 to the reverse complement (RC) of the corresponding region in IL28A. Locations of the genotyping assay primers are shaded and the rs12979860 SNP is boxed and highlighted in red.
Figure 4.
Allelic discrimination plot for the rs12979860 genotyping assay.
Allelic discrimination plot generated by the SDS 2.3 software (Applied Biosystems Inc.) for the rs12979860 genotyping assay using the 48 sample DNA panel. Red and blue circles represent the two homozygous genotypes (T/T and C/C), the green circles represent heterozygous genotype (C/T) and the black squares represent no template control.