Schematic showing IL28 genes, SNP locations and areas of sequence homology.

<p>Illustration of the relative locations of the <i>IL28A</i> and <i>IL28B</i> 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 <i>IL28B</i> region, whereas SNPs highlighted in other colors were present in the <i>IL28B</i> region as well as a corresponding region in <i>IL28A</i>.</p

TaqMan® amplification primers and detection probes for the rs12979860 genotyping assay.

<p>Nucleotides that gave the amplifying primers their specificity for <i>IL28B</i> are shown in bold underlined. The SNP location in the probes is indicated by the underlined nucleotide in larger font.</p

Sequence alignments surrounding six of the treatment response associated SNPs.

<p>Alignment comparing 50 bp sequence surrounding SNP locations in <i>IL28B</i> reference sequence from NCBI genome build 37 and the corresponding reverse complement regions of <i>IL28A</i> reference sequence (RC ref). SNP identifiers (color coded to match <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029983#pone-0029983-g001" target="_blank">Figure 1</a>) 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.</p

Details of PCR amplicons used to examine SNP locations in <i>IL28B</i> and the corresponding reverse complement (RC) regions of <i>IL28A</i>.

<p>Details of PCR amplicons used to examine SNP locations in <i>IL28B</i> and the corresponding reverse complement (RC) regions of <i>IL28A</i>.</p

Allele frequencies of <i>IL28B</i> SNPs and corresponding regions of <i>IL28A</i>.

<p>Allele frequencies of <i>IL28B</i> SNPs and corresponding regions of <i>IL28A</i>.</p

Allele frequencies of SNPs unique to <i>IL28B</i> region.

<p>Allele frequencies of SNPs unique to <i>IL28B</i> region.</p

Allelic discrimination plot for the rs12979860 genotyping assay.

<p>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.</p

Sequence alignment of <i>IL28B</i> and <i>IL28A</i> used to design the rs12979860 genotyping assay.

<p>Clustal W alignment of a portion of the <i>IL28B</i> gene surrounding rs12979860 to the reverse complement (RC) of the corresponding region in <i>IL28A</i>. Locations of the genotyping assay primers are shaded and the rs12979860 SNP is boxed and highlighted in red.</p

Quantile–quantile plots for the six different variant burden analysis methods.

<p>Quantile–quantile plots are shown for: (a) AMELIA, (b) CCRaVAT, (c) fixed filter test, minor allele frequency <0.05, (d) Madsen-Browning with polyphen weights, (e) Han and Pan aSumtest, (f) SSU, sum-of-squares test (Han and Pan).</p

Details of the SNVs identified in TUK1 and TUK2 samples.

<p>The number of SNVs detected is shown according to their functional consequences, for the TUK1 and TUK2 samples.</p