CD6 expression on different cell types segregated by non-synonymous CD6 haplotypes, as analyzed by FACS.

<p>A total of 27 PBMC samples representing each of the three haplotypes from the two non-synonymous SNPs rs11230563 and rs2074225 were analysed for CD6 expression on the different cell subsets. The y-axis represents the median fluorescence intensity (MFI) while the x-axis represents the three different haplotypes; i.e. the CC haplotype that confers protection, CT associated with risk and TT conferring mild risk. The distinct subpopulations were identified using different surface markers as listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062376#pone.0062376.s009" target="_blank">Table S4</a>. The markers CD3 and CD56 were used to identify T cells (CD4+/CD8+ CD3⁺ CD56⁻), NK (CD3⁻ CD56⁺), and NKT (CD3⁺ CD56⁺) cell subsets; CD45RA, CD27 and CD28 were used to distinguish naïve (CD45RA⁺ CD27⁺ CD28⁺), central memory cells (CD45RA⁻ CD27⁺) and effector memory cells (CD45RA⁻ CD27⁻ CD28⁺), as well as the terminally differentiated effector memory cells (TEMRA, CD45RA⁺ CD27⁻ CD28⁻); while CD56 and CD16 were used to identify the NK CD56dim (CD56^int CD16⁺) and the CD56bright (CD56^hi CD16) cells.</p

LD values (<i>D</i>’/<i>r²</i> values) between each of the 14 SNP markers genotyped in the Spanish-Basque population.

<p>The figure represents a comparison of the LD values between the 14 SNPs genotyped in the northern Spanish-Basque population (<i>D</i>’/<i>r²</i> values) using the values from the CEU 1000 genomes project and from the data generated from the Spanish-Basque population (823 cases/814 controls). The values in white are the <i>D’</i>/<i>r²</i> values from the CEU 1000 Genomes Project, while the blue-shaded ones are generated for the northern Spanish-Basque dataset using Haploview software (version 4.2).</p

Replication and combined analysis of the most significant SNPs.

<p><i>Abbreviations</i>: CMH = Cochran-Mantel-Haenszel test, BD = Breslow-Day test, OR = Odds ratio, CI = Confidence interval.</p>(1)<p>The risk alleles (with respect to the Basque dataset) are underlined.</p>(2)<p>The ORs are represented for the risk alleles found in the first-stage screen.</p>(3)<p>rs11230563 was included because it is a non-synonymous SNP that substitutes R225W, and showed a trend towards association in the first stage screen.</p>(4)<p>rs650258 was included based on the association observed in the Basque dataset.</p