Number of classical HLA alleles and polymorphic amino acid positions in the HLA reference panel.

<p>Number of classical HLA alleles and polymorphic amino acid positions in the HLA reference panel.</p

Frequencies and disease effect sizes of imputed and genotyped <i>HLA-DRB1</i> alleles.

<p>We revisited our previous rheumatoid arthritis association studies using either typed SNPs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112546#pone.0112546-Kim1" target="_blank">[16]</a> or HLA alleles <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112546#pone.0112546-Bang1" target="_blank">[17]</a>. After imputing HLA variants from the SNP-based dataset, (A) frequencies and (B) disease effect sizes of the imputed classical alleles of <i>HLA-DRB1</i> were compared with those of genotyped classical alleles in the HLA-based dataset.</p

Concordance rates using various reference panels.

<p>SNPs present in 9 different commercial arrays were extracted for imputing the HLA alleles from the HapMap3 r2 dataset of East Asian (CHB + JPT) individuals. Each subset was imputed for <i>HLA-A</i>, <i>-B</i>, <i>-C</i>, <i>-DQB1</i> and <i>-DRB1</i> using the Korean reference panel. Concordance rates (y-axis) were plotted against the proportion of reference-panel SNPs that were present in each subset (x-axis).</p

Concordance rates between imputed and genotyped alleles.

<p>* Reference panel and test datasets were randomly assigned 100 times from all 413 Korean subjects and the mean concordance rate was calculated by 100 independent imputations using each of the 100 reference panel and test dataset pairs.</p><p>** For consistency of panel size between Korean and European panels, the mean concordance rate was calculated by 100 independent imputations using 100 different subsets (n = 413) of the European reference panel.</p><p>Concordance rates between imputed and genotyped alleles.</p

Additional file 1: Table S1. of Biological function integrated prediction of severe radiographic progression in rheumatoid arthritis: a nested case control study

Characteristics of study populations. Table S2. GWAS results for severe radiographic progression (p <1.0 × 10–3). Table S3. List of the top 85 SNPs and their related genes selected by a post-GWAS approach. Table S4 Sensitivity, specificity, and positive predictive value of the final models. (DOCX 77 kb

Additional file 1: Table S1. of An HLA-C amino-acid variant in addition to HLA-B*27 confers risk for ankylosing spondylitis in the Korean population

Effect estimates for each residue at HLA-B amino-acid positions 70, 97, and 114. Table S2. Association of HLA-B amino-acid position 97 with ankylosing spondylitis in Korean and European populations. (PDF 84 kb

Concordance rate between imputed and actual allele of HLA genes^a.

<p>Concordance rate between imputed and actual allele of HLA genes<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150283#t001fn001" target="_blank">^a</a>.</p

Distributions of p values for disease associations of HLA-DRB variants.

<p>P values for all variants of <i>HLA-DRB1</i>, <i>HLA</i>-<i>DRB3</i>, <i>HLA</i>-<i>DRB4</i> and <i>HLA</i>-<i>DRB5</i> were calculated by unconditional and conditional analyses testing associations with RA and SLE. The most significant association in unconditional analyses was identified at HLA-DRβ1 amino-acid position (AA) 11 and AA13 in both RA <b>(A)</b> and SLE <b>(C)</b>. After conditioning on all reported disease-associated amino-acid positions of HLA-DRβ1 (11, 13, 71, and 74 in RA and 11, 13, and 26 in SLE), no additional association with p < 5 × 10⁻⁸ was identified in RA <b>(B)</b> or SLE <b>(D)</b>. Variants with the lowest p value are shown for each HLA-DRB gene.</p